PLUMED-NEST

Project ID: plumID:21.049
Source: 3ad_cycle/plumed.7.dat
Originally used with PLUMED version: 2.6
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

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../PathCV.cpp
The LOAD action with label  calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps ENERGYthe units of energy=kcal/mol

phi: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomsphic: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15 COSINE calculate cosine instead of dihedral
The TORSION action with label phic calculates the following quantities:
 Quantity   
 Description  
phic.value
the TORSION involving these atomsphis: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The CUSTOM action with label phis calculates the following quantities:
 Quantity   
 Description  
phis.value
an arbitrary functionpsi: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomspsic: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17 COSINE calculate cosine instead of dihedral
The TORSION action with label psic calculates the following quantities:
 Quantity   
 Description  
psic.value
the TORSION involving these atomspsis: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The CUSTOM action with label psis calculates the following quantities:
 Quantity   
 Description  
psis.value
an arbitrary functionPATHCVThis action is not part of PLUMED and was included by using a LOAD command More details LABEL=pcv ARG=phic,phis,psic,psis INFILE=in_cycle.input HALFLIFE=1000 PACE=250 WALKERS_RSTRIDE=250 WALKERS_ID=7 WALKERS_N=8 WALKERS_DIR=.

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pcv.z ATthe positions of the wall=0.0  KAPPAthe force constant for the wall=50.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=tube

The UPPER_WALLS action with label tube calculates the following quantities:
 Quantity   
 Description  
tube.bias
the instantaneous value of the bias potential
tube.force2
the instantaneous value of the squared force due to this bias potentialc: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=-1
The CONSTANT action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the constant value that was read from the plumed inputs: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=pcv.s,c COEFFICIENTS the coefficients of the arguments in your function=2.,1. PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-1,1

The COMBINE action with label s calculates the following quantities:
 Quantity   
 Description  
s.value
a linear compbinationRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=anchor ARGthe values the harmonic restraint acts upon=phi,psi ATthe position of the restraint=1.1,-0.8 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50.0,50.0

The RESTRAINT action with label anchor calculates the following quantities:
 Quantity   
 Description  
anchor.bias
the instantaneous value of the bias potential
anchor.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=10 ARGthe labels of the values that you would like to print to the file=phic,phis,psic,psis,phi,psi,s,pcv.s,pcv.z,anchor.bias,tube.bias FILEthe name of the file on which to output these quantities=./COLVAR