PLUMED-NEST

Project ID: plumID:21.029
Source: ala3/unbiased/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
The MOLINFO action with label  calculates something
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

energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the value calculated by this action: 
ENERGY
Calculate 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:   
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
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms:   
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
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms:   
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
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms:   
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
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms:   
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
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms:   
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





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
STRIDE
 the frequency with which the quantities of interest should be output
=100
FILE
the name of the file on which to output these quantities
=COLVAR
... PRINT