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

MOLINFO
This 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 
STRUCTURE
a file in pdb format containing a reference structure
=ala3.pdb
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=500

energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details
 
phi1:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitypsi1:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantityphi2:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitypsi2:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantityphi3:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantitypsi3:   
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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 a scalar quantity
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=phi2 
FILE
the name of the file containing the external potential
=factor1.grid 
LABEL
a 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 potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=phi1 
FILE
the name of the file containing the external potential
=factor2.grid 
LABEL
a 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 potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=phi3 
FILE
the name of the file containing the external potential
=factor3.grid 
LABEL
a 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 potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=psi2 
FILE
the name of the file containing the external potential
=factor4.grid 
LABEL
a 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 potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=psi3 
FILE
the name of the file containing the external potential
=factor5.grid 
LABEL
a 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 potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=psi1 
FILE
the name of the file containing the external potential
=factor6.grid 
LABEL
a 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 potential
PRINT
Print quantities to a file. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=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
FILE
the name of the file on which to output these quantities
=COLVAR
... PRINT