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 somethingr1The COM action with label r1 calculates the following quantities:
 Quantity   
 Type   
 Description  
r1
atoms
virtual atom calculated by COM action: 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
r2The COM action with label r2 calculates the following quantities:
 Quantity   
 Type   
 Description  
r2
atoms
virtual atom calculated by COM action: 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

c1The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the value of the coordination: 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 --- INCLUDEIncludes 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 somethingphi0The TORSION action with label phi0 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi0
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=24,4,3,1

# psi
psi0The TORSION action with label psi0 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi0
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=26,24,4,3
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,1,31,29

# omega
omega0The TORSION action with label omega0 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega0
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,1,31

# chi-1
chi0The TORSION action with label chi0 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi0
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,7,9
chi1The TORSION action with label chi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,29,34,36

# chi-2
chi20The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi20
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,7,13,14
chi21The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi21
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=29,34,40,41

# --- End of included input --- INCLUDEIncludes 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 somethingimp0The TORSION action with label imp0 calculates the following quantities:
 Quantity   
 Type   
 Description  
imp0
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,8,9,13
imp1The TORSION action with label imp1 calculates the following quantities:
 Quantity   
 Type   
 Description  
imp1
scalar
the TORSION involving these atoms: 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
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: 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 
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. 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=restraintThe RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Type   
 Description  
restraint.bias
scalar
the instantaneous value of the bias potential
restraint.force2
scalar
the instantaneous value of the squared force due to this bias potential
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. 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  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0,0.0

PBMETADUsed 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=pbThe PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Type   
 Description  
pb.bias
scalar
the instantaneous value of the bias potential
	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

PRINTPrint 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