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 appear in the definition of this center=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 VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=6,1 AXIStwo atoms that define an axis=6,10 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=6,1 AXIStwo atoms that define an axis=20,7 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 FMT the format that should be used to output real numbers=%6.5f
... PRINT

ENDPLUMEDTerminate plumed input. More details