PLUMED-NEST

Project ID: plumID:23.007
Source: plumed-nest/nrpe2/plumed.dat
Originally used with PLUMED version: 2.4.2
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

#! vim:ft=plumed
#RESTART  
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-50

The WHOLEMOLECULES action with label  calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cn.dat
# The command:
# INCLUDE FILE=cn.dat
# ensures PLUMED loads the contents of the file called cn.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label cn.dat calculates somethingr1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=13,22 #res 1 and 10 agg in trial 1
The COM action with label r1 calculates somethingr2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=40,49

The COM action with label r2 calculates somethingc1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10

# --- End of included input --- The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the value of the coordinationINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cv.dat
# The command:
# INCLUDE FILE=cv.dat
# ensures PLUMED loads the contents of the file called cv.dat
# The contents of this file are shown below (click the red comment to hide them).
# dihedrals
# phi
The INCLUDE action with label cv.dat calculates somethingphi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=24,4,3,1

# psi
The TORSION action with label phi0 calculates the following quantities:
 Quantity   
 Description  
phi0.value
the TORSION involving these atomspsi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=26,24,4,3
The TORSION action with label psi0 calculates the following quantities:
 Quantity   
 Description  
psi0.value
the TORSION involving these atomspsi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,1,31,29

# omega
The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Description  
psi1.value
the TORSION involving these atomsomega0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,1,31

# chi-1
The TORSION action with label omega0 calculates the following quantities:
 Quantity   
 Description  
omega0.value
the TORSION involving these atomschi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,7,9
The TORSION action with label chi0 calculates the following quantities:
 Quantity   
 Description  
chi0.value
the TORSION involving these atomschi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,29,34,36

# chi-2
The TORSION action with label chi1 calculates the following quantities:
 Quantity   
 Description  
chi1.value
the TORSION involving these atomschi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,7,13,14
The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Description  
chi20.value
the TORSION involving these atomschi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=29,34,40,41

# --- End of included input --- The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Description  
chi21.value
the TORSION involving these atomsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=imp.dat
# The command:
# INCLUDE FILE=imp.dat
# ensures PLUMED loads the contents of the file called imp.dat
# The contents of this file are shown below (click the red comment to hide them).
# dihedrals
# improper
The INCLUDE action with label imp.dat calculates somethingimp0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,8,9,13
The TORSION action with label imp0 calculates the following quantities:
 Quantity   
 Description  
imp0.value
the TORSION involving these atomsimp1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=34,35,36,40
#PRINT ARG=* STRIDE=50 FILE=DRIVER
# --- End of included input --- 
# rg
The TORSION action with label imp1 calculates the following quantities:
 Quantity   
 Description  
imp1.value
the TORSION involving these atomsrg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,3,4,29,31


# prevent r->s transition 
The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightsRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=imp0,imp1 ATthe position of the restraint=0.7,0.7 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=150,150 LABELa label for the action so that its output can be referenced in the input to other actions=restraint

The RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Description  
restraint.bias
the instantaneous value of the bias potential
restraint.force2
the instantaneous value of the squared force due to this bias potentialPBMETADUsed to performed Parallel Bias metadynamics. More details ...
	ARGthe labels of the scalars on which the bias will act=c1,rg,omega0,phi0,psi0,psi1,chi0,chi1
	SIGMAthe widths of the Gaussian hills=0.5,0.1,0.35,0.35,0.35,0.35,0.35,0.35
	HEIGHTthe height of the Gaussian hills, one for all biases=2.5 #kj/mol
  PACEthe frequency for hill addition, one for all biases=500
	BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=50
	GRID_MINthe lower bounds for the grid=-1,-1,-pi,-pi,-pi,-pi,-pi,-pi
	GRID_MAXthe upper bounds for the grid=20,20,pi,pi,pi,pi,pi,pi
	LABELa label for the action so that its output can be referenced in the input to other actions=pb
	FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_c1,HILLS_rg,HILLS_omega0,HILLS_phi0,HILLS_psi0,HILLS_psi1,HILLS_chi0,HILLS_chi1
... PBMETAD

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.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=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR