PLUMED-NEST-TEST-SITE

Project ID: plumID:21.030
Source: plumed-nest/npm/ab.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#! vim:ft=plumed

#alphaD- cis
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=-1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=-1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=-1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=-1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=-1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=-1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=-1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=-1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=-1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=-1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=-1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_minusThe ALPHABETA action with label alpha_d_minus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=-1.57
# ATOMS2=1,29,28,26 REFERENCE2=-1.57
# ATOMS3=26,49,48,46 REFERENCE3=-1.57
# ATOMS4=46,69,68,66 REFERENCE4=-1.57
# ATOMS5=66,89,88,86 REFERENCE5=-1.57
# ATOMS6=86,109,108,106 REFERENCE6=-1.57
# ATOMS7=106,129,128,126 REFERENCE7=-1.57
# ATOMS8=126,149,148,146 REFERENCE8=-1.57
# ATOMS9=146,169,168,166 REFERENCE9=-1.57
# ATOMS10=166,189,188,186 REFERENCE10=-1.57
# ATOMS11=186,209,208,206 REFERENCE11=-1.57
# ATOMS12=23,21,4,3 REFERENCE12=3.14
# ATOMS13=3,1,29,28 REFERENCE13=3.14
# ATOMS14=28,26,49,48 REFERENCE14=3.14
# ATOMS15=48,46,69,68 REFERENCE15=3.14
# ATOMS16=68,66,89,88 REFERENCE16=3.14
# ATOMS17=88,86,109,108 REFERENCE17=3.14
# ATOMS18=108,106,129,128 REFERENCE18=3.14
# ATOMS19=128,126,149,148 REFERENCE19=3.14
# ATOMS20=148,146,169,168 REFERENCE20=3.14
# ATOMS21=168,166,189,188 REFERENCE21=3.14
# ATOMS22=188,186,209,208 REFERENCE22=3.14
# ATOMS23=208,206,228,226 REFERENCE23=3.14
# ATOMS24=4,3,1,29 REFERENCE24=0
# ATOMS25=29,28,26,49 REFERENCE25=0
# ATOMS26=49,48,46,69 REFERENCE26=0
# ATOMS27=69,68,66,89 REFERENCE27=0
# ATOMS28=89,88,86,109 REFERENCE28=0
# ATOMS29=109,108,106,129 REFERENCE29=0
# ATOMS30=129,128,126,149 REFERENCE30=0
# ATOMS31=149,148,146,169 REFERENCE31=0
# ATOMS32=169,168,166,189 REFERENCE32=0
# ATOMS33=189,188,186,209 REFERENCE33=0
# ATOMS34=209,208,206,228 REFERENCE34=0
# LABEL=alpha_d_minus
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_d_minus_torsionsThe TORSION action with label alpha_d_minus_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_d_minus_refThe CONSTANT action with label alpha_d_minus_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,0,0,0,0,0,0,0,0,0,0,0
alpha_d_minus_coeffThe CONSTANT action with label alpha_d_minus_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_d_minus_combThe COMBINE action with label alpha_d_minus_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_d_minus_torsions,alpha_d_minus_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_minus_cosThe CUSTOM action with label alpha_d_minus_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_d_minus_comb,alpha_d_minus_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_minusThe SUM action with label alpha_d_minus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_d_minus_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#alphaD- trans
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=-1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=-1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=-1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=-1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=-1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=-1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=-1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=-1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=-1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=-1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=-1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_minus_transThe ALPHABETA action with label alpha_d_minus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=-1.57
# ATOMS2=1,29,28,26 REFERENCE2=-1.57
# ATOMS3=26,49,48,46 REFERENCE3=-1.57
# ATOMS4=46,69,68,66 REFERENCE4=-1.57
# ATOMS5=66,89,88,86 REFERENCE5=-1.57
# ATOMS6=86,109,108,106 REFERENCE6=-1.57
# ATOMS7=106,129,128,126 REFERENCE7=-1.57
# ATOMS8=126,149,148,146 REFERENCE8=-1.57
# ATOMS9=146,169,168,166 REFERENCE9=-1.57
# ATOMS10=166,189,188,186 REFERENCE10=-1.57
# ATOMS11=186,209,208,206 REFERENCE11=-1.57
# ATOMS12=23,21,4,3 REFERENCE12=3.14
# ATOMS13=3,1,29,28 REFERENCE13=3.14
# ATOMS14=28,26,49,48 REFERENCE14=3.14
# ATOMS15=48,46,69,68 REFERENCE15=3.14
# ATOMS16=68,66,89,88 REFERENCE16=3.14
# ATOMS17=88,86,109,108 REFERENCE17=3.14
# ATOMS18=108,106,129,128 REFERENCE18=3.14
# ATOMS19=128,126,149,148 REFERENCE19=3.14
# ATOMS20=148,146,169,168 REFERENCE20=3.14
# ATOMS21=168,166,189,188 REFERENCE21=3.14
# ATOMS22=188,186,209,208 REFERENCE22=3.14
# ATOMS23=208,206,228,226 REFERENCE23=3.14
# ATOMS24=4,3,1,29 REFERENCE24=3.14
# ATOMS25=29,28,26,49 REFERENCE25=3.14
# ATOMS26=49,48,46,69 REFERENCE26=3.14
# ATOMS27=69,68,66,89 REFERENCE27=3.14
# ATOMS28=89,88,86,109 REFERENCE28=3.14
# ATOMS29=109,108,106,129 REFERENCE29=3.14
# ATOMS30=129,128,126,149 REFERENCE30=3.14
# ATOMS31=149,148,146,169 REFERENCE31=3.14
# ATOMS32=169,168,166,189 REFERENCE32=3.14
# ATOMS33=189,188,186,209 REFERENCE33=3.14
# ATOMS34=209,208,206,228 REFERENCE34=3.14
# LABEL=alpha_d_minus_trans
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_d_minus_trans_torsionsThe TORSION action with label alpha_d_minus_trans_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_d_minus_trans_refThe CONSTANT action with label alpha_d_minus_trans_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,-1.57,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14
alpha_d_minus_trans_coeffThe CONSTANT action with label alpha_d_minus_trans_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_d_minus_trans_combThe COMBINE action with label alpha_d_minus_trans_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_d_minus_trans_torsions,alpha_d_minus_trans_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_minus_trans_cosThe CUSTOM action with label alpha_d_minus_trans_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_d_minus_trans_comb,alpha_d_minus_trans_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_minus_transThe SUM action with label alpha_d_minus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_minus_trans
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_d_minus_trans_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#alphaD+ cis
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_plusThe ALPHABETA action with label alpha_d_plus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=1.57
# ATOMS2=1,29,28,26 REFERENCE2=1.57
# ATOMS3=26,49,48,46 REFERENCE3=1.57
# ATOMS4=46,69,68,66 REFERENCE4=1.57
# ATOMS5=66,89,88,86 REFERENCE5=1.57
# ATOMS6=86,109,108,106 REFERENCE6=1.57
# ATOMS7=106,129,128,126 REFERENCE7=1.57
# ATOMS8=126,149,148,146 REFERENCE8=1.57
# ATOMS9=146,169,168,166 REFERENCE9=1.57
# ATOMS10=166,189,188,186 REFERENCE10=1.57
# ATOMS11=186,209,208,206 REFERENCE11=1.57
# ATOMS12=23,21,4,3 REFERENCE12=3.14
# ATOMS13=3,1,29,28 REFERENCE13=3.14
# ATOMS14=28,26,49,48 REFERENCE14=3.14
# ATOMS15=48,46,69,68 REFERENCE15=3.14
# ATOMS16=68,66,89,88 REFERENCE16=3.14
# ATOMS17=88,86,109,108 REFERENCE17=3.14
# ATOMS18=108,106,129,128 REFERENCE18=3.14
# ATOMS19=128,126,149,148 REFERENCE19=3.14
# ATOMS20=148,146,169,168 REFERENCE20=3.14
# ATOMS21=168,166,189,188 REFERENCE21=3.14
# ATOMS22=188,186,209,208 REFERENCE22=3.14
# ATOMS23=208,206,228,226 REFERENCE23=3.14
# ATOMS24=4,3,1,29 REFERENCE24=0
# ATOMS25=29,28,26,49 REFERENCE25=0
# ATOMS26=49,48,46,69 REFERENCE26=0
# ATOMS27=69,68,66,89 REFERENCE27=0
# ATOMS28=89,88,86,109 REFERENCE28=0
# ATOMS29=109,108,106,129 REFERENCE29=0
# ATOMS30=129,128,126,149 REFERENCE30=0
# ATOMS31=149,148,146,169 REFERENCE31=0
# ATOMS32=169,168,166,189 REFERENCE32=0
# ATOMS33=189,188,186,209 REFERENCE33=0
# ATOMS34=209,208,206,228 REFERENCE34=0
# LABEL=alpha_d_plus
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_d_plus_torsionsThe TORSION action with label alpha_d_plus_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_d_plus_refThe CONSTANT action with label alpha_d_plus_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,0,0,0,0,0,0,0,0,0,0,0
alpha_d_plus_coeffThe CONSTANT action with label alpha_d_plus_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_d_plus_combThe COMBINE action with label alpha_d_plus_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_d_plus_torsions,alpha_d_plus_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_plus_cosThe CUSTOM action with label alpha_d_plus_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_d_plus_comb,alpha_d_plus_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_plusThe SUM action with label alpha_d_plus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_d_plus_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#alphaD+ trans
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_plus_transThe ALPHABETA action with label alpha_d_plus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=1.57
# ATOMS2=1,29,28,26 REFERENCE2=1.57
# ATOMS3=26,49,48,46 REFERENCE3=1.57
# ATOMS4=46,69,68,66 REFERENCE4=1.57
# ATOMS5=66,89,88,86 REFERENCE5=1.57
# ATOMS6=86,109,108,106 REFERENCE6=1.57
# ATOMS7=106,129,128,126 REFERENCE7=1.57
# ATOMS8=126,149,148,146 REFERENCE8=1.57
# ATOMS9=146,169,168,166 REFERENCE9=1.57
# ATOMS10=166,189,188,186 REFERENCE10=1.57
# ATOMS11=186,209,208,206 REFERENCE11=1.57
# ATOMS12=23,21,4,3 REFERENCE12=3.14
# ATOMS13=3,1,29,28 REFERENCE13=3.14
# ATOMS14=28,26,49,48 REFERENCE14=3.14
# ATOMS15=48,46,69,68 REFERENCE15=3.14
# ATOMS16=68,66,89,88 REFERENCE16=3.14
# ATOMS17=88,86,109,108 REFERENCE17=3.14
# ATOMS18=108,106,129,128 REFERENCE18=3.14
# ATOMS19=128,126,149,148 REFERENCE19=3.14
# ATOMS20=148,146,169,168 REFERENCE20=3.14
# ATOMS21=168,166,189,188 REFERENCE21=3.14
# ATOMS22=188,186,209,208 REFERENCE22=3.14
# ATOMS23=208,206,228,226 REFERENCE23=3.14
# ATOMS24=4,3,1,29 REFERENCE24=3.14
# ATOMS25=29,28,26,49 REFERENCE25=3.14
# ATOMS26=49,48,46,69 REFERENCE26=3.14
# ATOMS27=69,68,66,89 REFERENCE27=3.14
# ATOMS28=89,88,86,109 REFERENCE28=3.14
# ATOMS29=109,108,106,129 REFERENCE29=3.14
# ATOMS30=129,128,126,149 REFERENCE30=3.14
# ATOMS31=149,148,146,169 REFERENCE31=3.14
# ATOMS32=169,168,166,189 REFERENCE32=3.14
# ATOMS33=189,188,186,209 REFERENCE33=3.14
# ATOMS34=209,208,206,228 REFERENCE34=3.14
# LABEL=alpha_d_plus_trans
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_d_plus_trans_torsionsThe TORSION action with label alpha_d_plus_trans_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_d_plus_trans_refThe CONSTANT action with label alpha_d_plus_trans_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,1.57,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14
alpha_d_plus_trans_coeffThe CONSTANT action with label alpha_d_plus_trans_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_d_plus_trans_combThe COMBINE action with label alpha_d_plus_trans_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_d_plus_trans_torsions,alpha_d_plus_trans_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_plus_trans_cosThe CUSTOM action with label alpha_d_plus_trans_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_d_plus_trans_comb,alpha_d_plus_trans_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_d_plus_transThe SUM action with label alpha_d_plus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_d_plus_trans
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_d_plus_trans_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# alpha+ cis
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_plusThe ALPHABETA action with label alpha_plus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=0.87
# ATOMS2=1,29,28,26 REFERENCE2=0.87
# ATOMS3=26,49,48,46 REFERENCE3=0.87
# ATOMS4=46,69,68,66 REFERENCE4=0.87
# ATOMS5=66,89,88,86 REFERENCE5=0.87
# ATOMS6=86,109,108,106 REFERENCE6=0.87
# ATOMS7=106,129,128,126 REFERENCE7=0.87
# ATOMS8=126,149,148,146 REFERENCE8=0.87
# ATOMS9=146,169,168,166 REFERENCE9=0.87
# ATOMS10=166,189,188,186 REFERENCE10=0.87
# ATOMS11=186,209,208,206 REFERENCE11=0.87
# ATOMS12=23,21,4,3 REFERENCE12=1.0
# ATOMS13=3,1,29,28 REFERENCE13=1.0
# ATOMS14=28,26,49,48 REFERENCE14=1.0
# ATOMS15=48,46,69,68 REFERENCE15=1.0
# ATOMS16=68,66,89,88 REFERENCE16=1.0
# ATOMS17=88,86,109,108 REFERENCE17=1.0
# ATOMS18=108,106,129,128 REFERENCE18=1.0
# ATOMS19=128,126,149,148 REFERENCE19=1.0
# ATOMS20=148,146,169,168 REFERENCE20=1.0
# ATOMS21=168,166,189,188 REFERENCE21=1.0
# ATOMS22=188,186,209,208 REFERENCE22=1.0
# ATOMS23=208,206,228,226 REFERENCE23=1.0
# ATOMS24=4,3,1,29 REFERENCE24=0
# ATOMS25=29,28,26,49 REFERENCE25=0
# ATOMS26=49,48,46,69 REFERENCE26=0
# ATOMS27=69,68,66,89 REFERENCE27=0
# ATOMS28=89,88,86,109 REFERENCE28=0
# ATOMS29=109,108,106,129 REFERENCE29=0
# ATOMS30=129,128,126,149 REFERENCE30=0
# ATOMS31=149,148,146,169 REFERENCE31=0
# ATOMS32=169,168,166,189 REFERENCE32=0
# ATOMS33=189,188,186,209 REFERENCE33=0
# ATOMS34=209,208,206,228 REFERENCE34=0
# LABEL=alpha_plus
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_plus_torsionsThe TORSION action with label alpha_plus_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_plus_refThe CONSTANT action with label alpha_plus_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0,0,0,0,0,0,0,0,0,0,0
alpha_plus_coeffThe CONSTANT action with label alpha_plus_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_plus_combThe COMBINE action with label alpha_plus_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_plus_torsions,alpha_plus_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_plus_cosThe CUSTOM action with label alpha_plus_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_plus_comb,alpha_plus_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_plusThe SUM action with label alpha_plus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_plus_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# alpha+ trans
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_plus_transThe ALPHABETA action with label alpha_plus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=0.87
# ATOMS2=1,29,28,26 REFERENCE2=0.87
# ATOMS3=26,49,48,46 REFERENCE3=0.87
# ATOMS4=46,69,68,66 REFERENCE4=0.87
# ATOMS5=66,89,88,86 REFERENCE5=0.87
# ATOMS6=86,109,108,106 REFERENCE6=0.87
# ATOMS7=106,129,128,126 REFERENCE7=0.87
# ATOMS8=126,149,148,146 REFERENCE8=0.87
# ATOMS9=146,169,168,166 REFERENCE9=0.87
# ATOMS10=166,189,188,186 REFERENCE10=0.87
# ATOMS11=186,209,208,206 REFERENCE11=0.87
# ATOMS12=23,21,4,3 REFERENCE12=1.0
# ATOMS13=3,1,29,28 REFERENCE13=1.0
# ATOMS14=28,26,49,48 REFERENCE14=1.0
# ATOMS15=48,46,69,68 REFERENCE15=1.0
# ATOMS16=68,66,89,88 REFERENCE16=1.0
# ATOMS17=88,86,109,108 REFERENCE17=1.0
# ATOMS18=108,106,129,128 REFERENCE18=1.0
# ATOMS19=128,126,149,148 REFERENCE19=1.0
# ATOMS20=148,146,169,168 REFERENCE20=1.0
# ATOMS21=168,166,189,188 REFERENCE21=1.0
# ATOMS22=188,186,209,208 REFERENCE22=1.0
# ATOMS23=208,206,228,226 REFERENCE23=1.0
# ATOMS24=4,3,1,29 REFERENCE24=3.14
# ATOMS25=29,28,26,49 REFERENCE25=3.14
# ATOMS26=49,48,46,69 REFERENCE26=3.14
# ATOMS27=69,68,66,89 REFERENCE27=3.14
# ATOMS28=89,88,86,109 REFERENCE28=3.14
# ATOMS29=109,108,106,129 REFERENCE29=3.14
# ATOMS30=129,128,126,149 REFERENCE30=3.14
# ATOMS31=149,148,146,169 REFERENCE31=3.14
# ATOMS32=169,168,166,189 REFERENCE32=3.14
# ATOMS33=189,188,186,209 REFERENCE33=3.14
# ATOMS34=209,208,206,228 REFERENCE34=3.14
# LABEL=alpha_plus_trans
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_plus_trans_torsionsThe TORSION action with label alpha_plus_trans_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_plus_trans_refThe CONSTANT action with label alpha_plus_trans_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,0.87,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14
alpha_plus_trans_coeffThe CONSTANT action with label alpha_plus_trans_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_plus_trans_combThe COMBINE action with label alpha_plus_trans_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_plus_trans_torsions,alpha_plus_trans_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_plus_trans_cosThe CUSTOM action with label alpha_plus_trans_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_plus_trans_comb,alpha_plus_trans_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_plus_transThe SUM action with label alpha_plus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_plus_trans
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_plus_trans_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# alpha- cis
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=-0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=-0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=-0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=-0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=-0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=-0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=-0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=-0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=-0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=-0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=-0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=-1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=-1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=-1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=-1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=-1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=-1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=-1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=-1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=-1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=-1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=-1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=-1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_minusThe ALPHABETA action with label alpha_minus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=-0.87
# ATOMS2=1,29,28,26 REFERENCE2=-0.87
# ATOMS3=26,49,48,46 REFERENCE3=-0.87
# ATOMS4=46,69,68,66 REFERENCE4=-0.87
# ATOMS5=66,89,88,86 REFERENCE5=-0.87
# ATOMS6=86,109,108,106 REFERENCE6=-0.87
# ATOMS7=106,129,128,126 REFERENCE7=-0.87
# ATOMS8=126,149,148,146 REFERENCE8=-0.87
# ATOMS9=146,169,168,166 REFERENCE9=-0.87
# ATOMS10=166,189,188,186 REFERENCE10=-0.87
# ATOMS11=186,209,208,206 REFERENCE11=-0.87
# ATOMS12=23,21,4,3 REFERENCE12=-1.0
# ATOMS13=3,1,29,28 REFERENCE13=-1.0
# ATOMS14=28,26,49,48 REFERENCE14=-1.0
# ATOMS15=48,46,69,68 REFERENCE15=-1.0
# ATOMS16=68,66,89,88 REFERENCE16=-1.0
# ATOMS17=88,86,109,108 REFERENCE17=-1.0
# ATOMS18=108,106,129,128 REFERENCE18=-1.0
# ATOMS19=128,126,149,148 REFERENCE19=-1.0
# ATOMS20=148,146,169,168 REFERENCE20=-1.0
# ATOMS21=168,166,189,188 REFERENCE21=-1.0
# ATOMS22=188,186,209,208 REFERENCE22=-1.0
# ATOMS23=208,206,228,226 REFERENCE23=-1.0
# ATOMS24=4,3,1,29 REFERENCE24=0
# ATOMS25=29,28,26,49 REFERENCE25=0
# ATOMS26=49,48,46,69 REFERENCE26=0
# ATOMS27=69,68,66,89 REFERENCE27=0
# ATOMS28=89,88,86,109 REFERENCE28=0
# ATOMS29=109,108,106,129 REFERENCE29=0
# ATOMS30=129,128,126,149 REFERENCE30=0
# ATOMS31=149,148,146,169 REFERENCE31=0
# ATOMS32=169,168,166,189 REFERENCE32=0
# ATOMS33=189,188,186,209 REFERENCE33=0
# ATOMS34=209,208,206,228 REFERENCE34=0
# LABEL=alpha_minus
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_minus_torsionsThe TORSION action with label alpha_minus_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_minus_refThe CONSTANT action with label alpha_minus_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0,0,0,0,0,0,0,0,0,0,0
alpha_minus_coeffThe CONSTANT action with label alpha_minus_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_minus_combThe COMBINE action with label alpha_minus_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_minus_torsions,alpha_minus_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_minus_cosThe CUSTOM action with label alpha_minus_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_minus_comb,alpha_minus_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_minusThe SUM action with label alpha_minus calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_minus_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
# alpha- trans
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=-0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=-0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=-0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=-0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=-0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=-0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=-0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=-0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=-0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=-0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=-0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=-1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=-1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=-1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=-1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=-1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=-1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=-1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=-1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=-1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=-1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=-1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=-1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_minus_transThe ALPHABETA action with label alpha_minus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=-0.87
# ATOMS2=1,29,28,26 REFERENCE2=-0.87
# ATOMS3=26,49,48,46 REFERENCE3=-0.87
# ATOMS4=46,69,68,66 REFERENCE4=-0.87
# ATOMS5=66,89,88,86 REFERENCE5=-0.87
# ATOMS6=86,109,108,106 REFERENCE6=-0.87
# ATOMS7=106,129,128,126 REFERENCE7=-0.87
# ATOMS8=126,149,148,146 REFERENCE8=-0.87
# ATOMS9=146,169,168,166 REFERENCE9=-0.87
# ATOMS10=166,189,188,186 REFERENCE10=-0.87
# ATOMS11=186,209,208,206 REFERENCE11=-0.87
# ATOMS12=23,21,4,3 REFERENCE12=-1.0
# ATOMS13=3,1,29,28 REFERENCE13=-1.0
# ATOMS14=28,26,49,48 REFERENCE14=-1.0
# ATOMS15=48,46,69,68 REFERENCE15=-1.0
# ATOMS16=68,66,89,88 REFERENCE16=-1.0
# ATOMS17=88,86,109,108 REFERENCE17=-1.0
# ATOMS18=108,106,129,128 REFERENCE18=-1.0
# ATOMS19=128,126,149,148 REFERENCE19=-1.0
# ATOMS20=148,146,169,168 REFERENCE20=-1.0
# ATOMS21=168,166,189,188 REFERENCE21=-1.0
# ATOMS22=188,186,209,208 REFERENCE22=-1.0
# ATOMS23=208,206,228,226 REFERENCE23=-1.0
# ATOMS24=4,3,1,29 REFERENCE24=3.14
# ATOMS25=29,28,26,49 REFERENCE25=3.14
# ATOMS26=49,48,46,69 REFERENCE26=3.14
# ATOMS27=69,68,66,89 REFERENCE27=3.14
# ATOMS28=89,88,86,109 REFERENCE28=3.14
# ATOMS29=109,108,106,129 REFERENCE29=3.14
# ATOMS30=129,128,126,149 REFERENCE30=3.14
# ATOMS31=149,148,146,169 REFERENCE31=3.14
# ATOMS32=169,168,166,189 REFERENCE32=3.14
# ATOMS33=189,188,186,209 REFERENCE33=3.14
# ATOMS34=209,208,206,228 REFERENCE34=3.14
# LABEL=alpha_minus_trans
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
alpha_minus_trans_torsionsThe TORSION action with label alpha_minus_trans_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
alpha_minus_trans_refThe CONSTANT action with label alpha_minus_trans_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-0.87,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14
alpha_minus_trans_coeffThe CONSTANT action with label alpha_minus_trans_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
alpha_minus_trans_combThe COMBINE action with label alpha_minus_trans_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=alpha_minus_trans_torsions,alpha_minus_trans_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_minus_trans_cosThe CUSTOM action with label alpha_minus_trans_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=alpha_minus_trans_comb,alpha_minus_trans_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alpha_minus_transThe SUM action with label alpha_minus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_minus_trans
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_minus_trans_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#c7beta+ cis
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=-1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=-1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=-1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=-1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=-1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=-1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=-1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=-1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=-1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=-1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=-1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=-1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_plusThe ALPHABETA action with label c7beta_plus calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=2.09
# ATOMS2=1,29,28,26 REFERENCE2=2.09
# ATOMS3=26,49,48,46 REFERENCE3=2.09
# ATOMS4=46,69,68,66 REFERENCE4=2.09
# ATOMS5=66,89,88,86 REFERENCE5=2.09
# ATOMS6=86,109,108,106 REFERENCE6=2.09
# ATOMS7=106,129,128,126 REFERENCE7=2.09
# ATOMS8=126,149,148,146 REFERENCE8=2.09
# ATOMS9=146,169,168,166 REFERENCE9=2.09
# ATOMS10=166,189,188,186 REFERENCE10=2.09
# ATOMS11=186,209,208,206 REFERENCE11=2.09
# ATOMS12=23,21,4,3 REFERENCE12=-1.3
# ATOMS13=3,1,29,28 REFERENCE13=-1.3
# ATOMS14=28,26,49,48 REFERENCE14=-1.3
# ATOMS15=48,46,69,68 REFERENCE15=-1.3
# ATOMS16=68,66,89,88 REFERENCE16=-1.3
# ATOMS17=88,86,109,108 REFERENCE17=-1.3
# ATOMS18=108,106,129,128 REFERENCE18=-1.3
# ATOMS19=128,126,149,148 REFERENCE19=-1.3
# ATOMS20=148,146,169,168 REFERENCE20=-1.3
# ATOMS21=168,166,189,188 REFERENCE21=-1.3
# ATOMS22=188,186,209,208 REFERENCE22=-1.3
# ATOMS23=208,206,228,226 REFERENCE23=-1.3
# ATOMS24=4,3,1,29 REFERENCE24=0
# ATOMS25=29,28,26,49 REFERENCE25=0
# ATOMS26=49,48,46,69 REFERENCE26=0
# ATOMS27=69,68,66,89 REFERENCE27=0
# ATOMS28=89,88,86,109 REFERENCE28=0
# ATOMS29=109,108,106,129 REFERENCE29=0
# ATOMS30=129,128,126,149 REFERENCE30=0
# ATOMS31=149,148,146,169 REFERENCE31=0
# ATOMS32=169,168,166,189 REFERENCE32=0
# ATOMS33=189,188,186,209 REFERENCE33=0
# ATOMS34=209,208,206,228 REFERENCE34=0
# LABEL=c7beta_plus
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
c7beta_plus_torsionsThe TORSION action with label c7beta_plus_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
c7beta_plus_refThe CONSTANT action with label c7beta_plus_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,0,0,0,0,0,0,0,0,0,0,0
c7beta_plus_coeffThe CONSTANT action with label c7beta_plus_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
c7beta_plus_combThe COMBINE action with label c7beta_plus_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c7beta_plus_torsions,c7beta_plus_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_plus_cosThe CUSTOM action with label c7beta_plus_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c7beta_plus_comb,c7beta_plus_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_plusThe SUM action with label c7beta_plus calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c7beta_plus_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#c7beta+ trans
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=-1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=-1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=-1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=-1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=-1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=-1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=-1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=-1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=-1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=-1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=-1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=-1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_plus_transThe ALPHABETA action with label c7beta_plus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=2.09
# ATOMS2=1,29,28,26 REFERENCE2=2.09
# ATOMS3=26,49,48,46 REFERENCE3=2.09
# ATOMS4=46,69,68,66 REFERENCE4=2.09
# ATOMS5=66,89,88,86 REFERENCE5=2.09
# ATOMS6=86,109,108,106 REFERENCE6=2.09
# ATOMS7=106,129,128,126 REFERENCE7=2.09
# ATOMS8=126,149,148,146 REFERENCE8=2.09
# ATOMS9=146,169,168,166 REFERENCE9=2.09
# ATOMS10=166,189,188,186 REFERENCE10=2.09
# ATOMS11=186,209,208,206 REFERENCE11=2.09
# ATOMS12=23,21,4,3 REFERENCE12=-1.3
# ATOMS13=3,1,29,28 REFERENCE13=-1.3
# ATOMS14=28,26,49,48 REFERENCE14=-1.3
# ATOMS15=48,46,69,68 REFERENCE15=-1.3
# ATOMS16=68,66,89,88 REFERENCE16=-1.3
# ATOMS17=88,86,109,108 REFERENCE17=-1.3
# ATOMS18=108,106,129,128 REFERENCE18=-1.3
# ATOMS19=128,126,149,148 REFERENCE19=-1.3
# ATOMS20=148,146,169,168 REFERENCE20=-1.3
# ATOMS21=168,166,189,188 REFERENCE21=-1.3
# ATOMS22=188,186,209,208 REFERENCE22=-1.3
# ATOMS23=208,206,228,226 REFERENCE23=-1.3
# ATOMS24=4,3,1,29 REFERENCE24=3.14
# ATOMS25=29,28,26,49 REFERENCE25=3.14
# ATOMS26=49,48,46,69 REFERENCE26=3.14
# ATOMS27=69,68,66,89 REFERENCE27=3.14
# ATOMS28=89,88,86,109 REFERENCE28=3.14
# ATOMS29=109,108,106,129 REFERENCE29=3.14
# ATOMS30=129,128,126,149 REFERENCE30=3.14
# ATOMS31=149,148,146,169 REFERENCE31=3.14
# ATOMS32=169,168,166,189 REFERENCE32=3.14
# ATOMS33=189,188,186,209 REFERENCE33=3.14
# ATOMS34=209,208,206,228 REFERENCE34=3.14
# LABEL=c7beta_plus_trans
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
c7beta_plus_trans_torsionsThe TORSION action with label c7beta_plus_trans_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
c7beta_plus_trans_refThe CONSTANT action with label c7beta_plus_trans_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,2.09,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,-1.3,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14
c7beta_plus_trans_coeffThe CONSTANT action with label c7beta_plus_trans_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
c7beta_plus_trans_combThe COMBINE action with label c7beta_plus_trans_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c7beta_plus_trans_torsions,c7beta_plus_trans_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_plus_trans_cosThe CUSTOM action with label c7beta_plus_trans_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c7beta_plus_trans_comb,c7beta_plus_trans_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_plus_transThe SUM action with label c7beta_plus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_plus_trans
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c7beta_plus_trans_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#c7beta- cis
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=-2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=-2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=-2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=-2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=-2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=-2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=-2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=-2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=-2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=-2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=-2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_minusThe ALPHABETA action with label c7beta_minus calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=-2.09
# ATOMS2=1,29,28,26 REFERENCE2=-2.09
# ATOMS3=26,49,48,46 REFERENCE3=-2.09
# ATOMS4=46,69,68,66 REFERENCE4=-2.09
# ATOMS5=66,89,88,86 REFERENCE5=-2.09
# ATOMS6=86,109,108,106 REFERENCE6=-2.09
# ATOMS7=106,129,128,126 REFERENCE7=-2.09
# ATOMS8=126,149,148,146 REFERENCE8=-2.09
# ATOMS9=146,169,168,166 REFERENCE9=-2.09
# ATOMS10=166,189,188,186 REFERENCE10=-2.09
# ATOMS11=186,209,208,206 REFERENCE11=-2.09
# ATOMS12=23,21,4,3 REFERENCE12=1.3
# ATOMS13=3,1,29,28 REFERENCE13=1.3
# ATOMS14=28,26,49,48 REFERENCE14=1.3
# ATOMS15=48,46,69,68 REFERENCE15=1.3
# ATOMS16=68,66,89,88 REFERENCE16=1.3
# ATOMS17=88,86,109,108 REFERENCE17=1.3
# ATOMS18=108,106,129,128 REFERENCE18=1.3
# ATOMS19=128,126,149,148 REFERENCE19=1.3
# ATOMS20=148,146,169,168 REFERENCE20=1.3
# ATOMS21=168,166,189,188 REFERENCE21=1.3
# ATOMS22=188,186,209,208 REFERENCE22=1.3
# ATOMS23=208,206,228,226 REFERENCE23=1.3
# ATOMS24=4,3,1,29 REFERENCE24=0
# ATOMS25=29,28,26,49 REFERENCE25=0
# ATOMS26=49,48,46,69 REFERENCE26=0
# ATOMS27=69,68,66,89 REFERENCE27=0
# ATOMS28=89,88,86,109 REFERENCE28=0
# ATOMS29=109,108,106,129 REFERENCE29=0
# ATOMS30=129,128,126,149 REFERENCE30=0
# ATOMS31=149,148,146,169 REFERENCE31=0
# ATOMS32=169,168,166,189 REFERENCE32=0
# ATOMS33=189,188,186,209 REFERENCE33=0
# ATOMS34=209,208,206,228 REFERENCE34=0
# LABEL=c7beta_minus
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
c7beta_minus_torsionsThe TORSION action with label c7beta_minus_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
c7beta_minus_refThe CONSTANT action with label c7beta_minus_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,0,0,0,0,0,0,0,0,0,0,0
c7beta_minus_coeffThe CONSTANT action with label c7beta_minus_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
c7beta_minus_combThe COMBINE action with label c7beta_minus_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c7beta_minus_torsions,c7beta_minus_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_minus_cosThe CUSTOM action with label c7beta_minus_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c7beta_minus_comb,c7beta_minus_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_minusThe SUM action with label c7beta_minus calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c7beta_minus_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
#c7beta+ trans
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=21,4,3,1 REFERENCE1the reference values for each of the torsional angles=-2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,29,28,26 REFERENCE2the reference values for each of the torsional angles=-2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=26,49,48,46 REFERENCE3the reference values for each of the torsional angles=-2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=46,69,68,66 REFERENCE4the reference values for each of the torsional angles=-2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=66,89,88,86 REFERENCE5the reference values for each of the torsional angles=-2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=86,109,108,106 REFERENCE6the reference values for each of the torsional angles=-2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=106,129,128,126 REFERENCE7the reference values for each of the torsional angles=-2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=126,149,148,146 REFERENCE8the reference values for each of the torsional angles=-2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=146,169,168,166 REFERENCE9the reference values for each of the torsional angles=-2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=166,189,188,186 REFERENCE10the reference values for each of the torsional angles=-2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=186,209,208,206 REFERENCE11the reference values for each of the torsional angles=-2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=23,21,4,3 REFERENCE12the reference values for each of the torsional angles=1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,29,28 REFERENCE13the reference values for each of the torsional angles=1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=28,26,49,48 REFERENCE14the reference values for each of the torsional angles=1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=48,46,69,68 REFERENCE15the reference values for each of the torsional angles=1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=68,66,89,88 REFERENCE16the reference values for each of the torsional angles=1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=88,86,109,108 REFERENCE17the reference values for each of the torsional angles=1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=108,106,129,128 REFERENCE18the reference values for each of the torsional angles=1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=128,126,149,148 REFERENCE19the reference values for each of the torsional angles=1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=148,146,169,168 REFERENCE20the reference values for each of the torsional angles=1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=168,166,189,188 REFERENCE21the reference values for each of the torsional angles=1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=188,186,209,208 REFERENCE22the reference values for each of the torsional angles=1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=208,206,228,226 REFERENCE23the reference values for each of the torsional angles=1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,29 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=29,28,26,49 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=49,48,46,69 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=69,68,66,89 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=89,88,86,109 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=109,108,106,129 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=129,128,126,149 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=149,148,146,169 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=169,168,166,189 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=189,188,186,209 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=209,208,206,228 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_minus_transThe ALPHABETA action with label c7beta_minus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans
scalar
the alpha beta CV
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# ATOMS1=21,4,3,1 REFERENCE1=-2.09
# ATOMS2=1,29,28,26 REFERENCE2=-2.09
# ATOMS3=26,49,48,46 REFERENCE3=-2.09
# ATOMS4=46,69,68,66 REFERENCE4=-2.09
# ATOMS5=66,89,88,86 REFERENCE5=-2.09
# ATOMS6=86,109,108,106 REFERENCE6=-2.09
# ATOMS7=106,129,128,126 REFERENCE7=-2.09
# ATOMS8=126,149,148,146 REFERENCE8=-2.09
# ATOMS9=146,169,168,166 REFERENCE9=-2.09
# ATOMS10=166,189,188,186 REFERENCE10=-2.09
# ATOMS11=186,209,208,206 REFERENCE11=-2.09
# ATOMS12=23,21,4,3 REFERENCE12=1.3
# ATOMS13=3,1,29,28 REFERENCE13=1.3
# ATOMS14=28,26,49,48 REFERENCE14=1.3
# ATOMS15=48,46,69,68 REFERENCE15=1.3
# ATOMS16=68,66,89,88 REFERENCE16=1.3
# ATOMS17=88,86,109,108 REFERENCE17=1.3
# ATOMS18=108,106,129,128 REFERENCE18=1.3
# ATOMS19=128,126,149,148 REFERENCE19=1.3
# ATOMS20=148,146,169,168 REFERENCE20=1.3
# ATOMS21=168,166,189,188 REFERENCE21=1.3
# ATOMS22=188,186,209,208 REFERENCE22=1.3
# ATOMS23=208,206,228,226 REFERENCE23=1.3
# ATOMS24=4,3,1,29 REFERENCE24=3.14
# ATOMS25=29,28,26,49 REFERENCE25=3.14
# ATOMS26=49,48,46,69 REFERENCE26=3.14
# ATOMS27=69,68,66,89 REFERENCE27=3.14
# ATOMS28=89,88,86,109 REFERENCE28=3.14
# ATOMS29=109,108,106,129 REFERENCE29=3.14
# ATOMS30=129,128,126,149 REFERENCE30=3.14
# ATOMS31=149,148,146,169 REFERENCE31=3.14
# ATOMS32=169,168,166,189 REFERENCE32=3.14
# ATOMS33=189,188,186,209 REFERENCE33=3.14
# ATOMS34=209,208,206,228 REFERENCE34=3.14
# LABEL=c7beta_minus_trans
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
c7beta_minus_trans_torsionsThe TORSION action with label c7beta_minus_trans_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=21,4,3,1 ATOMS2the four atoms involved in the torsional angle=1,29,28,26 ATOMS3the four atoms involved in the torsional angle=26,49,48,46 ATOMS4the four atoms involved in the torsional angle=46,69,68,66 ATOMS5the four atoms involved in the torsional angle=66,89,88,86     # Action input conctinues with 29 further ATOMSn keywords, 
c7beta_minus_trans_refThe CONSTANT action with label c7beta_minus_trans_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,-2.09,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14,3.14
c7beta_minus_trans_coeffThe CONSTANT action with label c7beta_minus_trans_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
c7beta_minus_trans_combThe COMBINE action with label c7beta_minus_trans_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans_comb
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c7beta_minus_trans_torsions,c7beta_minus_trans_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_minus_trans_cosThe CUSTOM action with label c7beta_minus_trans_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c7beta_minus_trans_comb,c7beta_minus_trans_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c7beta_minus_transThe SUM action with label c7beta_minus_trans calculates the following quantities:
 Quantity   
 Type   
 Description  
c7beta_minus_trans
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c7beta_minus_trans_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---