PLUMED-NEST

Project ID: plumID:21.029
Source: ala3/parallel/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

energy: ENERGYCalculate the total potential energy of the simulation box. More details 
The ENERGY action with label energy calculates somethingphi1:   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
The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Description  
phi1.value
the TORSION involving these atomspsi1:   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
The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Description  
psi1.value
the TORSION involving these atomsphi2:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25    NOPBC ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Description  
phi2.value
the TORSION involving these atomspsi2:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=17,19,25,27    NOPBC ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Description  
psi2.value
the TORSION involving these atomsphi3:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35    NOPBC ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Description  
phi3.value
the TORSION involving these atomspsi3:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37    NOPBC ignore the periodic boundary conditions when calculating distances

The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Description  
psi3.value
the TORSION involving these atomsEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=phi2 FILEthe name of the file containing the external potential=factor1.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor1
The EXTERNAL action with label factor1 calculates the following quantities:
 Quantity   
 Description  
factor1.bias
the instantaneous value of the bias potentialEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=phi1 FILEthe name of the file containing the external potential=factor2.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor2
The EXTERNAL action with label factor2 calculates the following quantities:
 Quantity   
 Description  
factor2.bias
the instantaneous value of the bias potentialEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=phi3 FILEthe name of the file containing the external potential=factor3.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor3
The EXTERNAL action with label factor3 calculates the following quantities:
 Quantity   
 Description  
factor3.bias
the instantaneous value of the bias potentialEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=psi2 FILEthe name of the file containing the external potential=factor4.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor4
The EXTERNAL action with label factor4 calculates the following quantities:
 Quantity   
 Description  
factor4.bias
the instantaneous value of the bias potentialEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=psi3 FILEthe name of the file containing the external potential=factor5.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor5
The EXTERNAL action with label factor5 calculates the following quantities:
 Quantity   
 Description  
factor5.bias
the instantaneous value of the bias potentialEXTERNALCalculate a restraint that is defined on a grid that is read during start up More details ARGthe labels of the scalars on which the bias will act=psi1 FILEthe name of the file containing the external potential=factor6.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor6


The EXTERNAL action with label factor6 calculates the following quantities:
 Quantity   
 Description  
factor6.bias
the instantaneous value of the bias potentialPRINTPrint 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,factor5.bias,factor6.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