PLUMED-NEST-TEST-SITE

Project ID: plumID:20.009
Source: Ub4/plumed-cv.dat
Originally used with PLUMED version: 2.6
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

#SETTINGS NREPLICAS=2
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=template.pdb

The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-652

#ubi1
aThe CENTER_FAST action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75,77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150 NOPBC ignore the periodic boundary conditions when calculating distances
a1The CENTER_FAST action with label a1 calculates the following quantities:
 Quantity   
 Type   
 Description  
a1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75 NOPBC ignore the periodic boundary conditions when calculating distances
a2The CENTER_FAST action with label a2 calculates the following quantities:
 Quantity   
 Type   
 Description  
a2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150 NOPBC ignore the periodic boundary conditions when calculating distances
#ubi2
bThe CENTER_FAST action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313 NOPBC ignore the periodic boundary conditions when calculating distances
b1The CENTER_FAST action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238 NOPBC ignore the periodic boundary conditions when calculating distances
b2The CENTER_FAST action with label b2 calculates the following quantities:
 Quantity   
 Type   
 Description  
b2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313 NOPBC ignore the periodic boundary conditions when calculating distances
#ubi3
cThe CENTER_FAST action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401,403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476 NOPBC ignore the periodic boundary conditions when calculating distances
c1The CENTER_FAST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401 NOPBC ignore the periodic boundary conditions when calculating distances
c2The CENTER_FAST action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476 NOPBC ignore the periodic boundary conditions when calculating distances
#ubi4
eThe CENTER_FAST action with label e calculates the following quantities:
 Quantity   
 Type   
 Description  
e
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=490,492,494,496,500,502,505,507,509,511,512,515,517,519,521,523,525,527,529,531,533,535,537,539,541,543,545,548,549,552,554,556,558,561,563,564,566,568,570,572,574,576,579,581,583,587,588,589,592,594,596,598,600,601,604,606,608,610,612,616,618,620,622,625,627,629,631,633,637,639 NOPBC ignore the periodic boundary conditions when calculating distances
e1The CENTER_FAST action with label e1 calculates the following quantities:
 Quantity   
 Type   
 Description  
e1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=490,492,494,496,500,502,505,507,509,511,512,515,517,519,521,523,525,527,529,531,533,535,537,539,541,543,545,548,549,552,554,556,558,561,563,564 NOPBC ignore the periodic boundary conditions when calculating distances
e2The CENTER_FAST action with label e2 calculates the following quantities:
 Quantity   
 Type   
 Description  
e2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=566,568,570,572,574,576,579,581,583,587,588,589,592,594,596,598,600,601,604,606,608,610,612,616,618,620,622,625,627,629,631,633,637,639 NOPBC ignore the periodic boundary conditions when calculating distances

# distance between ubiquitins 
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,b NOPBC ignore the periodic boundary conditions when calculating distances
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,c NOPBC ignore the periodic boundary conditions when calculating distances
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,e NOPBC ignore the periodic boundary conditions when calculating distances
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=b,c NOPBC ignore the periodic boundary conditions when calculating distances
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=b,e NOPBC ignore the periodic boundary conditions when calculating distances
d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c,e NOPBC ignore the periodic boundary conditions when calculating distances


#relativ orientation
tor1The TORSION action with label tor1 calculates the following quantities:
 Quantity   
 Type   
 Description  
tor1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=a1,a2,b1,b2 NOPBC ignore the periodic boundary conditions when calculating distances
tor2The TORSION action with label tor2 calculates the following quantities:
 Quantity   
 Type   
 Description  
tor2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=a1,a2,c1,c2 NOPBC ignore the periodic boundary conditions when calculating distances
tor3The TORSION action with label tor3 calculates the following quantities:
 Quantity   
 Type   
 Description  
tor3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=a1,a2,e1,e2 NOPBC ignore the periodic boundary conditions when calculating distances
tor4The TORSION action with label tor4 calculates the following quantities:
 Quantity   
 Type   
 Description  
tor4
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=b1,b2,c1,c2 NOPBC ignore the periodic boundary conditions when calculating distances
tor5The TORSION action with label tor5 calculates the following quantities:
 Quantity   
 Type   
 Description  
tor5
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=b1,b2,e1,e2 NOPBC ignore the periodic boundary conditions when calculating distances
tor6The TORSION action with label tor6 calculates the following quantities:
 Quantity   
 Type   
 Description  
tor6
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=c1,c2,e1,e2 NOPBC ignore the periodic boundary conditions when calculating distances

#global radius

rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,3,5,7,11,13,16,18,20,22,23,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,59,60,63,65,67,69,72,74,75,77,79,81,83,85,87,90,92,94,98,99,100,103,105,107,109,111,112,115,117,119,121,123,127,129,131,133,136,138,140,142,144,148,150,152,154,157,159,162,163,164,166,168,170,174,176,179,181,183,185,186,189,191,193,195,197,199,201,203,205,207,209,211,213,215,217,219,222,223,226,228,230,232,235,237,238,240,242,244,246,248,250,253,255,257,261,262,263,266,268,270,272,274,275,278,280,282,284,286,290,292,294,296,299,301,303,305,307,311,313,315,317,320,322,325,326,327,329,331,333,337,339,342,344,346,348,349,352,354,356,358,360,362,364,366,368,370,372,374,376,378,380,382,385,386,389,391,393,395,398,400,401,403,405,407,409,411,413,416,418,420,424,425,426,429,431,433,435,437,438,441,443,445,447,449,453,455,457,459,462,464,466,468,470,474,476,478,480,483,485,488,489,490,492,494,496,500,502,505,507,509,511,512,515,517,519,521,523,525,527,529,531,533,535,537,539,541,543,545,548,549,552,554,556,558,561,563,564,566,568,570,572,574,576,579,581,583,587,588,589,592,594,596,598,600,601,604,606,608,610,612,616,618,620,622,625,627,629,631,633,637,639,641,643,646,648,651,652 NOPBC ignore the periodic boundary conditions when calculating distances

#linker angle
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 ...
LABELa label for the action so that its output can be referenced in the input to other actions=linktor1The ALPHABETA action with label linktor1 calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1
scalar
the alpha beta CV
REFERENCEthe reference values for each of the torsional angles=0
ATOMS1the atoms involved for each of the torsions you wish to calculate=150,152,154,157
ATOMS2the atoms involved for each of the torsions you wish to calculate=152,154,157,159
ATOMS3the atoms involved for each of the torsions you wish to calculate=154,157,159,162
ATOMS4the atoms involved for each of the torsions you wish to calculate=157,159,162,163
ATOMS5the atoms involved for each of the torsions you wish to calculate=159,162,163,164
ATOMS6the atoms involved for each of the torsions you wish to calculate=162,163,164,166
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# LABEL=linktor1
# REFERENCE=0
# ATOMS1=150,152,154,157
# ATOMS2=152,154,157,159
# ATOMS3=154,157,159,162
# ATOMS4=157,159,162,163
# ATOMS5=159,162,163,164
# ATOMS6=162,163,164,166
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
linktor1_torsionsThe TORSION action with label linktor1_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1_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=150,152,154,157 ATOMS2the four atoms involved in the torsional angle=152,154,157,159 ATOMS3the four atoms involved in the torsional angle=154,157,159,162 ATOMS4the four atoms involved in the torsional angle=157,159,162,163 ATOMS5the four atoms involved in the torsional angle=159,162,163,164     # Action input conctinues with 1 further ATOMSn keywords, 
linktor1_refThe CONSTANT action with label linktor1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1_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=0,0,0,0,0,0
linktor1_coeffThe CONSTANT action with label linktor1_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1_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
linktor1_combThe COMBINE action with label linktor1_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1_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=linktor1_torsions,linktor1_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
linktor1_cosThe CUSTOM action with label linktor1_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1_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=linktor1_comb,linktor1_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
linktor1The SUM action with label linktor1 calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor1
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=linktor1_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
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 ...
LABELa label for the action so that its output can be referenced in the input to other actions=linktor2The ALPHABETA action with label linktor2 calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2
scalar
the alpha beta CV
REFERENCEthe reference values for each of the torsional angles=0
ATOMS1the atoms involved for each of the torsions you wish to calculate=313,315,317,320
ATOMS2the atoms involved for each of the torsions you wish to calculate=315,317,320,322
ATOMS3the atoms involved for each of the torsions you wish to calculate=317,320,322,325
ATOMS4the atoms involved for each of the torsions you wish to calculate=320,322,325,326
ATOMS5the atoms involved for each of the torsions you wish to calculate=322,325,326,327
ATOMS6the atoms involved for each of the torsions you wish to calculate=325,326,327,329
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# LABEL=linktor2
# REFERENCE=0
# ATOMS1=313,315,317,320
# ATOMS2=315,317,320,322
# ATOMS3=317,320,322,325
# ATOMS4=320,322,325,326
# ATOMS5=322,325,326,327
# ATOMS6=325,326,327,329
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
linktor2_torsionsThe TORSION action with label linktor2_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2_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=313,315,317,320 ATOMS2the four atoms involved in the torsional angle=315,317,320,322 ATOMS3the four atoms involved in the torsional angle=317,320,322,325 ATOMS4the four atoms involved in the torsional angle=320,322,325,326 ATOMS5the four atoms involved in the torsional angle=322,325,326,327     # Action input conctinues with 1 further ATOMSn keywords, 
linktor2_refThe CONSTANT action with label linktor2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2_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=0,0,0,0,0,0
linktor2_coeffThe CONSTANT action with label linktor2_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2_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
linktor2_combThe COMBINE action with label linktor2_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2_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=linktor2_torsions,linktor2_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
linktor2_cosThe CUSTOM action with label linktor2_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2_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=linktor2_comb,linktor2_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
linktor2The SUM action with label linktor2 calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor2
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=linktor2_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
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 ...
LABELa label for the action so that its output can be referenced in the input to other actions=linktor3The ALPHABETA action with label linktor3 calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3
scalar
the alpha beta CV
REFERENCEthe reference values for each of the torsional angles=0
ATOMS1the atoms involved for each of the torsions you wish to calculate=476,478,480,483
ATOMS2the atoms involved for each of the torsions you wish to calculate=478,480,483,485
ATOMS3the atoms involved for each of the torsions you wish to calculate=480,483,485,488
ATOMS4the atoms involved for each of the torsions you wish to calculate=483,485,488,489
ATOMS5the atoms involved for each of the torsions you wish to calculate=485,488,489,490
ATOMS6the atoms involved for each of the torsions you wish to calculate=488,489,490,492
... ALPHABETA
# PLUMED interprets the command:
# ALPHABETA ...
# LABEL=linktor3
# REFERENCE=0
# ATOMS1=476,478,480,483
# ATOMS2=478,480,483,485
# ATOMS3=480,483,485,488
# ATOMS4=483,485,488,489
# ATOMS5=485,488,489,490
# ATOMS6=488,489,490,492
# ... ALPHABETA
# as follows (Click the red comment above to revert to the short version of the input):
linktor3_torsionsThe TORSION action with label linktor3_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3_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=476,478,480,483 ATOMS2the four atoms involved in the torsional angle=478,480,483,485 ATOMS3the four atoms involved in the torsional angle=480,483,485,488 ATOMS4the four atoms involved in the torsional angle=483,485,488,489 ATOMS5the four atoms involved in the torsional angle=485,488,489,490     # Action input conctinues with 1 further ATOMSn keywords, 
linktor3_refThe CONSTANT action with label linktor3_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3_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=0,0,0,0,0,0
linktor3_coeffThe CONSTANT action with label linktor3_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3_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
linktor3_combThe COMBINE action with label linktor3_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3_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=linktor3_torsions,linktor3_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
linktor3_cosThe CUSTOM action with label linktor3_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3_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=linktor3_comb,linktor3_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
linktor3The SUM action with label linktor3 calculates the following quantities:
 Quantity   
 Type   
 Description  
linktor3
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=linktor3_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 

SAXSCalculates SAXS intensity. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=test2The SAXS action with label test2 calculates the following quantities:
 Quantity   
 Type   
 Description  
test2.q-0
scalar
The # SAXS of q  This is the 0th of these quantities
test2.q-1
scalar
The # SAXS of q  This is the 1th of these quantities
test2.q-2
scalar
The # SAXS of q  This is the 2th of these quantities
test2.q-3
scalar
The # SAXS of q  This is the 3th of these quantities
test2.q-4
scalar
The # SAXS of q  This is the 4th of these quantities
test2.q-5
scalar
The # SAXS of q  This is the 5th of these quantities
test2.q-6
scalar
The # SAXS of q  This is the 6th of these quantities
test2.q-7
scalar
The # SAXS of q  This is the 7th of these quantities
test2.q-8
scalar
The # SAXS of q  This is the 8th of these quantities
test2.q-9
scalar
The # SAXS of q  This is the 9th of these quantities
test2.q-10
scalar
The # SAXS of q  This is the 10th of these quantities
test2.q-11
scalar
The # SAXS of q  This is the 11th of these quantities
test2.q-12
scalar
The # SAXS of q  This is the 12th of these quantities
test2.q-13
scalar
The # SAXS of q  This is the 13th of these quantities
test2.q-14
scalar
The # SAXS of q  This is the 14th of these quantities
test2.q-15
scalar
The # SAXS of q  This is the 15th of these quantities
test2.q-16
scalar
The # SAXS of q  This is the 16th of these quantities
test2.q-17
scalar
The # SAXS of q  This is the 17th of these quantities
test2.q-18
scalar
The # SAXS of q  This is the 18th of these quantities
test2.q-19
scalar
The # SAXS of q  This is the 19th of these quantities
test2.exp-0
scalar
The # experimental intensity  This is the 0th of these quantities
test2.exp-1
scalar
The # experimental intensity  This is the 1th of these quantities
test2.exp-2
scalar
The # experimental intensity  This is the 2th of these quantities
test2.exp-3
scalar
The # experimental intensity  This is the 3th of these quantities
test2.exp-4
scalar
The # experimental intensity  This is the 4th of these quantities
test2.exp-5
scalar
The # experimental intensity  This is the 5th of these quantities
test2.exp-6
scalar
The # experimental intensity  This is the 6th of these quantities
test2.exp-7
scalar
The # experimental intensity  This is the 7th of these quantities
test2.exp-8
scalar
The # experimental intensity  This is the 8th of these quantities
test2.exp-9
scalar
The # experimental intensity  This is the 9th of these quantities
test2.exp-10
scalar
The # experimental intensity  This is the 10th of these quantities
test2.exp-11
scalar
The # experimental intensity  This is the 11th of these quantities
test2.exp-12
scalar
The # experimental intensity  This is the 12th of these quantities
test2.exp-13
scalar
The # experimental intensity  This is the 13th of these quantities
test2.exp-14
scalar
The # experimental intensity  This is the 14th of these quantities
test2.exp-15
scalar
The # experimental intensity  This is the 15th of these quantities
test2.exp-16
scalar
The # experimental intensity  This is the 16th of these quantities
test2.exp-17
scalar
The # experimental intensity  This is the 17th of these quantities
test2.exp-18
scalar
The # experimental intensity  This is the 18th of these quantities
test2.exp-19
scalar
The # experimental intensity  This is the 19th of these quantities
ATOMSThe atoms to be included in the calculation, e=1-652
NOPBC Ignore the periodic boundary conditions when calculating distances

MARTINI Calculate SAXS for a Martini model

QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.02
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.03
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.04
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.05
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.06
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.07
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.08
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.09
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.11
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.12
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.13
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.14
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.15
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.16
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.17
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.18
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.19
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.21

 EXPINT1Add an experimental value for each q value=5.24833
 EXPINT2Add an experimental value for each q value=4.39027
 EXPINT3Add an experimental value for each q value=3.50363
 EXPINT4Add an experimental value for each q value=2.70379
 EXPINT5Add an experimental value for each q value=2.07676
 EXPINT6Add an experimental value for each q value=1.62809
 EXPINT7Add an experimental value for each q value=1.31061
 EXPINT8Add an experimental value for each q value=1.07411
 EXPINT9Add an experimental value for each q value=0.887992
EXPINT10Add an experimental value for each q value=0.738255
EXPINT11Add an experimental value for each q value=0.617356
EXPINT12Add an experimental value for each q value=0.518766
EXPINT13Add an experimental value for each q value=0.436834
EXPINT14Add an experimental value for each q value=0.367909
EXPINT15Add an experimental value for each q value=0.310039
EXPINT16Add an experimental value for each q value=0.261567
EXPINT17Add an experimental value for each q value=0.220234
EXPINT18Add an experimental value for each q value=0.183526
EXPINT19Add an experimental value for each q value=0.149622
EXPINT20Add an experimental value for each q value=0.117966
... SAXS
SAXSCalculates SAXS intensity. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=test2
ATOMSThe atoms to be included in the calculation, e=1-652
NOPBC Ignore the periodic boundary conditions when calculating distances

MARTINI Calculate SAXS for a Martini model

QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.02
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.03
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.04
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.05
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.06
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.07
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.08
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.09
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.11
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.12
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.13
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.14
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.15
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.16
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.17
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.18
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.19
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2
QVALUE20Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.21

 EXPINT1Add an experimental value for each q value=5.24833
 EXPINT2Add an experimental value for each q value=4.39027
 EXPINT3Add an experimental value for each q value=3.50363
 EXPINT4Add an experimental value for each q value=2.70379
 EXPINT5Add an experimental value for each q value=2.07676
 EXPINT6Add an experimental value for each q value=1.62809
 EXPINT7Add an experimental value for each q value=1.31061
 EXPINT8Add an experimental value for each q value=1.07411
 EXPINT9Add an experimental value for each q value=0.887992
EXPINT10Add an experimental value for each q value=0.738255
EXPINT11Add an experimental value for each q value=0.617356
EXPINT12Add an experimental value for each q value=0.518766
EXPINT13Add an experimental value for each q value=0.436834
EXPINT14Add an experimental value for each q value=0.367909
EXPINT15Add an experimental value for each q value=0.310039
EXPINT16Add an experimental value for each q value=0.261567
EXPINT17Add an experimental value for each q value=0.220234
EXPINT18Add an experimental value for each q value=0.183526
EXPINT19Add an experimental value for each q value=0.149622
EXPINT20Add an experimental value for each q value=0.117966
 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MGAUSS WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.0 SIGMA_MAX maximum value of the uncertainty parameter=10. DEVICEID Identifier of the GPU to be used=-1 SOLVDENS Density of the solvent to be used for the correction of atomistic form factors=0.334 SCALE_EXPINT Scaling value for experimental data normalization=1.0 SOLVATION_CORRECTION Solvation layer electron density correction (ONEBEAD only)=0.0 SOLVATION_STRIDE Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)=10 SASA_CUTOFF SASA value to consider a residue as exposed to the solvent (ONEBEAD only)=1.0 DEUTER_CONC Fraction of deuterated solvent=0. N Number of points in the resolution function integral=10
... SAXS

lsaxsThe STATS action with label lsaxs calculates the following quantities:
 Quantity   
 Type   
 Description  
lsaxs.sqdevsum
scalar
the sum of the squared deviations between arguments and parameters
lsaxs.corr
scalar
the correlation between arguments and parameters
lsaxs.slope
scalar
the slope of a linear fit between arguments and parameters
lsaxs.intercept
scalar
the intercept of a linear fit between arguments and parameters: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(test2\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(test2\.exp-.*)


PBMETADUsed to performed Parallel Bias metadynamics. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=biasThe PBMETAD action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias.bias
scalar
the instantaneous value of the bias potential
ARGthe labels of the scalars on which the bias will act=d1,d2,d3,d4,d5,d6,linktor1,linktor2,linktor3,rg,tor1,tor2,tor3,tor4,tor5,tor6
HEIGHTthe height of the Gaussian hills, one for all biases=0.075
PACEthe frequency for hill addition, one for all biases=200
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=40
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID.0,GRID.1,GRID.2,GRID.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8,GRID.9,GRID.10,GRID.11,GRID.12,GRID.13,GRID.14,GRID.15
GRID_WSTRIDEfrequency for dumping the grid=2000
#GRID_RFILES=GRID.0,GRID.1,GRID.2,GRID.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8,GRID.9,GRID.10,GRID.11,GRID.12,GRID.13,GRID.14,GRID.15
SIGMAthe widths of the Gaussian hills=1000
SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2

GRID_MINthe lower bounds for the grid=0,0,0,0,0,0,0,0,0,0,-pi,-pi,-pi,-pi,-pi,-pi
GRID_MAXthe upper bounds for the grid=7,14,18,7,14,7,6,6,6,7,pi,pi,pi,pi,pi,pi

WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
UPDATE_FROMOnly update this action from this time=2000
... PBMETAD

METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ...
SCALEDATA Set to TRUE if you want to sample a scaling factor common to all values and replicas
NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=MOUTLIERS
AVERAGINGStride for calculation of averaged weights and sigma_mean=100
ARGthe labels of the scalars on which the bias will act=(test2\.q-.*),bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(test2\.exp-.*)
SCALE_PRIOR either FLAT or GAUSSIAN=FLAT
ADDOFFSET Set to TRUE if you want to sample an offset common to all values and replicas
OFFSET_PRIOR either FLAT or GAUSSIAN=FLAT
OFFSET0 initial value of the offset=0 OFFSET_MINminimum value of the offset=-10 OFFSET_MAXmaximum value of the offset=10 DOFFSETmaximum MC move of the offset=0.01
SCALE0 initial value of the scaling factor=1.00 SCALE_MINminimum value of the scaling factor=0.8 SCALE_MAXmaximum value of the scaling factor=1.2 DSCALEmaximum MC move of the scaling factor=0.001
SIGMA0 initial value of the uncertainty parameter=0.01 SIGMA_MIN minimum value of the uncertainty parameter=0. SIGMA_MAX maximum value of the uncertainty parameter=0.05
OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM
LABELa label for the action so that its output can be referenced in the input to other actions=bqThe METAINFERENCE action with label bq calculates the following quantities:
 Quantity   
 Type   
 Description  
bq.bias
scalar
the instantaneous value of the bias potential
bq.biasDer
scalar
derivatives with respect to the bias
bq.weight
scalar
weights of the weighted average
bq.neff
scalar
effective number of replicas
bq.scale
scalar
scale parameter
bq.offset
scalar
offset parameter
bq.acceptScale
scalar
MC acceptance for scale value
bq.acceptSigma
scalar
MC acceptance for sigma values
bq.sigmaMean-0
scalar
uncertainty in the mean estimate  This is the 0th of these quantities
bq.sigma-0
scalar
uncertainty parameter  This is the 0th of these quantities
bq.sigmaMean-1
scalar
uncertainty in the mean estimate  This is the 1th of these quantities
bq.sigma-1
scalar
uncertainty parameter  This is the 1th of these quantities
bq.sigmaMean-2
scalar
uncertainty in the mean estimate  This is the 2th of these quantities
bq.sigma-2
scalar
uncertainty parameter  This is the 2th of these quantities
bq.sigmaMean-3
scalar
uncertainty in the mean estimate  This is the 3th of these quantities
bq.sigma-3
scalar
uncertainty parameter  This is the 3th of these quantities
bq.sigmaMean-4
scalar
uncertainty in the mean estimate  This is the 4th of these quantities
bq.sigma-4
scalar
uncertainty parameter  This is the 4th of these quantities
bq.sigmaMean-5
scalar
uncertainty in the mean estimate  This is the 5th of these quantities
bq.sigma-5
scalar
uncertainty parameter  This is the 5th of these quantities
bq.sigmaMean-6
scalar
uncertainty in the mean estimate  This is the 6th of these quantities
bq.sigma-6
scalar
uncertainty parameter  This is the 6th of these quantities
bq.sigmaMean-7
scalar
uncertainty in the mean estimate  This is the 7th of these quantities
bq.sigma-7
scalar
uncertainty parameter  This is the 7th of these quantities
bq.sigmaMean-8
scalar
uncertainty in the mean estimate  This is the 8th of these quantities
bq.sigma-8
scalar
uncertainty parameter  This is the 8th of these quantities
bq.sigmaMean-9
scalar
uncertainty in the mean estimate  This is the 9th of these quantities
bq.sigma-9
scalar
uncertainty parameter  This is the 9th of these quantities
bq.sigmaMean-10
scalar
uncertainty in the mean estimate  This is the 10th of these quantities
bq.sigma-10
scalar
uncertainty parameter  This is the 10th of these quantities
bq.sigmaMean-11
scalar
uncertainty in the mean estimate  This is the 11th of these quantities
bq.sigma-11
scalar
uncertainty parameter  This is the 11th of these quantities
bq.sigmaMean-12
scalar
uncertainty in the mean estimate  This is the 12th of these quantities
bq.sigma-12
scalar
uncertainty parameter  This is the 12th of these quantities
bq.sigmaMean-13
scalar
uncertainty in the mean estimate  This is the 13th of these quantities
bq.sigma-13
scalar
uncertainty parameter  This is the 13th of these quantities
bq.sigmaMean-14
scalar
uncertainty in the mean estimate  This is the 14th of these quantities
bq.sigma-14
scalar
uncertainty parameter  This is the 14th of these quantities
bq.sigmaMean-15
scalar
uncertainty in the mean estimate  This is the 15th of these quantities
bq.sigma-15
scalar
uncertainty parameter  This is the 15th of these quantities
bq.sigmaMean-16
scalar
uncertainty in the mean estimate  This is the 16th of these quantities
bq.sigma-16
scalar
uncertainty parameter  This is the 16th of these quantities
bq.sigmaMean-17
scalar
uncertainty in the mean estimate  This is the 17th of these quantities
bq.sigma-17
scalar
uncertainty parameter  This is the 17th of these quantities
bq.sigmaMean-18
scalar
uncertainty in the mean estimate  This is the 18th of these quantities
bq.sigma-18
scalar
uncertainty parameter  This is the 18th of these quantities
bq.sigmaMean-19
scalar
uncertainty in the mean estimate  This is the 19th of these quantities
bq.sigma-19
scalar
uncertainty parameter  This is the 19th of these quantities
WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000
STRIDEthe frequency with which the forces due to the bias should be calculated=5
... METAINFERENCE


ensaxsThe ENSEMBLE action with label ensaxs calculates the following quantities:
 Quantity   
 Type   
 Description  
ensaxs.test2.q-0
scalar
the average for argument test2.q-0
ensaxs.test2.q-1
scalar
the average for argument test2.q-1
ensaxs.test2.q-2
scalar
the average for argument test2.q-2
ensaxs.test2.q-3
scalar
the average for argument test2.q-3
ensaxs.test2.q-4
scalar
the average for argument test2.q-4
ensaxs.test2.q-5
scalar
the average for argument test2.q-5
ensaxs.test2.q-6
scalar
the average for argument test2.q-6
ensaxs.test2.q-7
scalar
the average for argument test2.q-7
ensaxs.test2.q-8
scalar
the average for argument test2.q-8
ensaxs.test2.q-9
scalar
the average for argument test2.q-9
ensaxs.test2.q-10
scalar
the average for argument test2.q-10
ensaxs.test2.q-11
scalar
the average for argument test2.q-11
ensaxs.test2.q-12
scalar
the average for argument test2.q-12
ensaxs.test2.q-13
scalar
the average for argument test2.q-13
ensaxs.test2.q-14
scalar
the average for argument test2.q-14
ensaxs.test2.q-15
scalar
the average for argument test2.q-15
ensaxs.test2.q-16
scalar
the average for argument test2.q-16
ensaxs.test2.q-17
scalar
the average for argument test2.q-17
ensaxs.test2.q-18
scalar
the average for argument test2.q-18
ensaxs.test2.q-19
scalar
the average for argument test2.q-19: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(test2\.q-.*),bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
statsqThe STATS action with label statsq calculates the following quantities:
 Quantity   
 Type   
 Description  
statsq.sqdevsum
scalar
the sum of the squared deviations between arguments and parameters
statsq.corr
scalar
the correlation between arguments and parameters
statsq.slope
scalar
the slope of a linear fit between arguments and parameters
statsq.intercept
scalar
the intercept of a linear fit between arguments and parameters: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(ensaxs\.test2\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(test2\.exp-.*)



FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(test2\.q-.*),(test2\.exp-.*) FILEthe name of the file on which to output these quantities=CV.dat STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=RESTRAINTS ARGthe labels of the values that you would like to print to the file=bq.* STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=q.dat ARGthe labels of the values that you would like to print to the file=statsq.*,lsaxs.* STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=Analyse.dat ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,linktor1,linktor2,linktor3,rg,tor1,tor2,tor3,tor4,tor5,tor6 STRIDE the frequency with which the quantities of interest should be output=100
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ENSAXS ARGthe labels of the values that you would like to print to the file=(ensaxs\.test2\.q-.*) STRIDE the frequency with which the quantities of interest should be output=100

enANAThe ENSEMBLE action with label enANA calculates the following quantities:
 Quantity   
 Type   
 Description  
enANA.d1
scalar
the average for argument d1
enANA.d2
scalar
the average for argument d2
enANA.d3
scalar
the average for argument d3
enANA.d4
scalar
the average for argument d4
enANA.d5
scalar
the average for argument d5
enANA.d6
scalar
the average for argument d6
enANA.linktor1
scalar
the average for argument linktor1
enANA.linktor2
scalar
the average for argument linktor2
enANA.linktor3
scalar
the average for argument linktor3
enANA.rg
scalar
the average for argument rg
enANA.tor1
scalar
the average for argument tor1
enANA.tor2
scalar
the average for argument tor2
enANA.tor3
scalar
the average for argument tor3
enANA.tor4
scalar
the average for argument tor4
enANA.tor5
scalar
the average for argument tor5
enANA.tor6
scalar
the average for argument tor6: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,linktor1,linktor2,linktor3,rg,tor1,tor2,tor3,tor4,tor5,tor6,bias.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ENANA ARGthe labels of the values that you would like to print to the file=enANA.* STRIDE the frequency with which the quantities of interest should be output=100