PLUMED-NEST

Project ID: plumID:19.075
Source: regtest/pycv/rt-f2/plumed.dat
Originally used with PLUMED version: 2.5.2-mod
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

# Copy of basic/rt13

g1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-10
The GROUP action with label g1 calculates somethingc1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details   ATOMSthe group of atoms that you are calculating the Gyration Tensor for=g1

The CENTER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the position of the center of masst1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,6,10,15
The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Description  
t1.value
the TORSION involving these atomst2: TORSIONCalculate one or multiple torsional angles. More details VECTOR1two atoms that define a vector=6,1 AXIStwo atoms that define an axis=6,10 VECTOR2two atoms that define a vector=10,15
The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Description  
t2.value
the TORSION involving these atomst3: TORSIONCalculate one or multiple torsional angles. More details VECTOR1two atoms that define a vector=6,1 AXIStwo atoms that define an axis=20,7 VECTOR2two atoms that define a vector=10,c1

The TORSION action with label t3 calculates the following quantities:
 Quantity   
 Description  
t3.value
the TORSION involving these atomscc1: PYTHONFUNCTIONThis action is not part of PLUMED and was included by using a LOAD command More details ARG=t1,t2,t3 IMPORT=pythonfunction FUNCTION=cc1 PERIODIC=NO
cc2: PYTHONFUNCTIONThis action is not part of PLUMED and was included by using a LOAD command More details ARG=t1,t2,t3 IMPORT=pythonfunction FUNCTION=cc2 PERIODIC=NO
cc3: PYTHONFUNCTIONThis action is not part of PLUMED and was included by using a LOAD command More details ARG=t1,t2    IMPORT=pythonfunction FUNCTION=cc3 PERIODIC=NO

# cc1: MATHEVAL ARG=t1,t2,t3 FUNC=x^2+y+0*z+1 PERIODIC=NO
# cc2: MATHEVAL ARG=t1,t2,t3 FUNC=0*x^3+0*y^3+0*z^3 PERIODIC=NO
# cc3: MATHEVAL ARG=t1,t2 FUNC=x^2+y^2 PERIODIC=NO

all: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=t1,t2,t3,cc1,cc2,cc3 VARthe names to give each of the arguments in the function=a1,a2,a3,a4,a5,a6 FUNCthe function you wish to evaluate={ (a1+a2+a3+a4+a5+a6) / 6.0 } PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The CUSTOM action with label all calculates the following quantities:
 Quantity   
 Description  
all.value
an arbitrary functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=all ATthe position of the restraint=0 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=1.0

The RESTRAINT action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ...
  STRIDE the frequency with which the quantities of interest should be output=2
  ARGthe labels of the values that you would like to print to the file=t1,t2,t3,cc1,cc2,cc3,all
  FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%6.5f
... PRINT

ENDPLUMEDTerminate plumed input. More details