Project ID: plumID:19.028
Source: ala/round1/plumed.1.dat
Originally used with PLUMED version: 2.3
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
phiThe TORSION action with label phi calculates the following quantities:| Quantity | Type | Description |
| phi | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15 NOPBC ignore the periodic boundary conditions when calculating distances
psiThe TORSION action with label psi calculates the following quantities:| Quantity | Type | Description |
| psi | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17 NOPBC ignore the periodic boundary conditions when calculating distances
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=5,7,9,15 REFERENCEthe 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=ab1_phiThe ALPHABETA action with label ab1_phi calculates the following quantities:| Quantity | Type | Description |
| ab1_phi | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=5,7,9,15 REFERENCE=0 LABEL=ab1_phi
ab1_phi_torsionsThe TORSION action with label ab1_phi_torsions calculates the following quantities:| Quantity | Type | Description |
| ab1_phi_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=5,7,9,15
ab1_phi_refThe CONSTANT action with label ab1_phi_ref calculates the following quantities:| Quantity | Type | Description |
| ab1_phi_ref | scalar | 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
ab1_phi_coeffThe CONSTANT action with label ab1_phi_coeff calculates the following quantities:| Quantity | Type | Description |
| ab1_phi_coeff | scalar | 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
ab1_phi_combThe COMBINE action with label ab1_phi_comb calculates the following quantities:| Quantity | Type | Description |
| ab1_phi_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=ab1_phi_torsions,ab1_phi_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
ab1_phi_cosThe CUSTOM action with label ab1_phi_cos calculates the following quantities:| Quantity | Type | Description |
| ab1_phi_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=ab1_phi_comb,ab1_phi_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
ab1_phiThe SUM action with label ab1_phi calculates the following quantities:| Quantity | Type | Description |
| ab1_phi | 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=ab1_phi_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 ATOMS1the atoms involved for each of the torsions you wish to calculate=5,7,9,15 REFERENCEthe reference values for each of the torsional angles=-1.5708 LABELa label for the action so that its output can be referenced in the input to other actions=ab2_phiThe ALPHABETA action with label ab2_phi calculates the following quantities:| Quantity | Type | Description |
| ab2_phi | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=5,7,9,15 REFERENCE=-1.5708 LABEL=ab2_phi
ab2_phi_torsionsThe TORSION action with label ab2_phi_torsions calculates the following quantities:| Quantity | Type | Description |
| ab2_phi_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=5,7,9,15
ab2_phi_refThe CONSTANT action with label ab2_phi_ref calculates the following quantities:| Quantity | Type | Description |
| ab2_phi_ref | scalar | 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=-1.5708
ab2_phi_coeffThe CONSTANT action with label ab2_phi_coeff calculates the following quantities:| Quantity | Type | Description |
| ab2_phi_coeff | scalar | 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
ab2_phi_combThe COMBINE action with label ab2_phi_comb calculates the following quantities:| Quantity | Type | Description |
| ab2_phi_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=ab2_phi_torsions,ab2_phi_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
ab2_phi_cosThe CUSTOM action with label ab2_phi_cos calculates the following quantities:| Quantity | Type | Description |
| ab2_phi_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=ab2_phi_comb,ab2_phi_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
ab2_phiThe SUM action with label ab2_phi calculates the following quantities:| Quantity | Type | Description |
| ab2_phi | 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=ab2_phi_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 ATOMS1the atoms involved for each of the torsions you wish to calculate=7,9,15,17 REFERENCEthe 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=ab1_psiThe ALPHABETA action with label ab1_psi calculates the following quantities:| Quantity | Type | Description |
| ab1_psi | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=7,9,15,17 REFERENCE=0 LABEL=ab1_psi
ab1_psi_torsionsThe TORSION action with label ab1_psi_torsions calculates the following quantities:| Quantity | Type | Description |
| ab1_psi_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=7,9,15,17
ab1_psi_refThe CONSTANT action with label ab1_psi_ref calculates the following quantities:| Quantity | Type | Description |
| ab1_psi_ref | scalar | 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
ab1_psi_coeffThe CONSTANT action with label ab1_psi_coeff calculates the following quantities:| Quantity | Type | Description |
| ab1_psi_coeff | scalar | 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
ab1_psi_combThe COMBINE action with label ab1_psi_comb calculates the following quantities:| Quantity | Type | Description |
| ab1_psi_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=ab1_psi_torsions,ab1_psi_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
ab1_psi_cosThe CUSTOM action with label ab1_psi_cos calculates the following quantities:| Quantity | Type | Description |
| ab1_psi_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=ab1_psi_comb,ab1_psi_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
ab1_psiThe SUM action with label ab1_psi calculates the following quantities:| Quantity | Type | Description |
| ab1_psi | 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=ab1_psi_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 ATOMS1the atoms involved for each of the torsions you wish to calculate=7,9,15,17 REFERENCEthe reference values for each of the torsional angles=-1.5708 LABELa label for the action so that its output can be referenced in the input to other actions=ab2_psiThe ALPHABETA action with label ab2_psi calculates the following quantities:| Quantity | Type | Description |
| ab2_psi | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=7,9,15,17 REFERENCE=-1.5708 LABEL=ab2_psi
ab2_psi_torsionsThe TORSION action with label ab2_psi_torsions calculates the following quantities:| Quantity | Type | Description |
| ab2_psi_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=7,9,15,17
ab2_psi_refThe CONSTANT action with label ab2_psi_ref calculates the following quantities:| Quantity | Type | Description |
| ab2_psi_ref | scalar | 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=-1.5708
ab2_psi_coeffThe CONSTANT action with label ab2_psi_coeff calculates the following quantities:| Quantity | Type | Description |
| ab2_psi_coeff | scalar | 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
ab2_psi_combThe COMBINE action with label ab2_psi_comb calculates the following quantities:| Quantity | Type | Description |
| ab2_psi_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=ab2_psi_torsions,ab2_psi_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
ab2_psi_cosThe CUSTOM action with label ab2_psi_cos calculates the following quantities:| Quantity | Type | Description |
| ab2_psi_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=ab2_psi_comb,ab2_psi_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
ab2_psiThe SUM action with label ab2_psi calculates the following quantities:| Quantity | Type | Description |
| ab2_psi | 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=ab2_psi_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=cos_phiThe COMBINE action with label cos_phi calculates the following quantities:| Quantity | Type | Description |
| cos_phi | scalar | a linear compbination |
ARGthe values input to this function=ab1_phi COEFFICIENTS the coefficients of the arguments in your function=2.0 PARAMETERS the parameters of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE
COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=sin_phiThe COMBINE action with label sin_phi calculates the following quantities:| Quantity | Type | Description |
| sin_phi | scalar | a linear compbination |
ARGthe values input to this function=ab2_phi COEFFICIENTS the coefficients of the arguments in your function=-2.0 PARAMETERS the parameters of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE
COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=cos_psiThe COMBINE action with label cos_psi calculates the following quantities:| Quantity | Type | Description |
| cos_psi | scalar | a linear compbination |
ARGthe values input to this function=ab1_psi COEFFICIENTS the coefficients of the arguments in your function=2.0 PARAMETERS the parameters of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE
COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=sin_psiThe COMBINE action with label sin_psi calculates the following quantities:| Quantity | Type | Description |
| sin_psi | scalar | a linear compbination |
ARGthe values input to this function=ab2_psi COEFFICIENTS the coefficients of the arguments in your function=-2.0 PARAMETERS the parameters of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=rc1The COMBINE action with label rc1 calculates the following quantities:| Quantity | Type | Description |
| rc1 | scalar | a linear compbination |
ARGthe values input to this function=cos_phi,sin_phi,cos_psi,sin_psi POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=0.2865360759350727,-0.09433915972557924,0.8925838462508046,-0.33509890710374146 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=rc1 FILEthe name of the file containing the external potential=static_bias.1.txt LABELa label for the action so that its output can be referenced in the input to other actions=external1The EXTERNAL action with label external1 calculates the following quantities:| Quantity | Type | Description |
| external1.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=rc1 FILEthe name of the file containing the external potential=static_bias.1.txt LABELa label for the action so that its output can be referenced in the input to other actions=external1 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cos_phi,sin_phi,cos_psi,sin_psi,phi,psi,rc1,external1.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=ala_T300_1
