PLUMED-NEST

Project ID: plumID:21.029
Source: ala3/FG/plumed.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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=ala3.pdb
The MOLINFO action with label  calculates somethingFLUSHThis 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=500

energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details 
phi1The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi1
scalar
the TORSION involving these atoms:   TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15       NOPBC ignore the periodic boundary conditions when calculating distances
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms:   TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17      NOPBC ignore the periodic boundary conditions when calculating distances
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms:   TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25    NOPBC ignore the periodic boundary conditions when calculating distances
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms:   TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=17,19,25,27    NOPBC ignore the periodic boundary conditions when calculating distances
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms:   TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35    NOPBC ignore the periodic boundary conditions when calculating distances
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms:   TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37    NOPBC ignore the periodic boundary conditions when calculating distances

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=psi1,phi2,phi1 FILEthe name of the file containing the external potential=factor1.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor1The EXTERNAL action with label factor1 calculates the following quantities:
 Quantity   
 Type   
 Description  
factor1.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=psi1,phi2,phi1 FILEthe name of the file containing the external potential=factor1.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor1  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
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=psi1,phi2,psi2 FILEthe name of the file containing the external potential=factor2.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor2The EXTERNAL action with label factor2 calculates the following quantities:
 Quantity   
 Type   
 Description  
factor2.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=psi1,phi2,psi2 FILEthe name of the file containing the external potential=factor2.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor2  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
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=psi1,psi3 FILEthe name of the file containing the external potential=factor3.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor3The EXTERNAL action with label factor3 calculates the following quantities:
 Quantity   
 Type   
 Description  
factor3.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=psi1,psi3 FILEthe name of the file containing the external potential=factor3.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor3  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
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=phi3,psi3 FILEthe name of the file containing the external potential=factor4.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor4The EXTERNAL action with label factor4 calculates the following quantities:
 Quantity   
 Type   
 Description  
factor4.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=phi3,psi3 FILEthe name of the file containing the external potential=factor4.grid NOSPLINE specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential LABELa label for the action so that its output can be referenced in the input to other actions=factor4  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=phi1,psi1,phi2,psi2,phi3,psi3,factor1.bias,factor2.bias,factor3.bias,factor4.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=COLVAR
... PRINT