PLUMED-NEST

Project ID: plumID:19.021
Source: ./Trajectories/EDS-flattening-enm/flatten-dihed-mean-target/meant_0.11/gatp-enm-12site_FEStart_eq175ns.range10_init0/gatp-enm-12site_FEStart_eq175ns.range10_init0.10ps.run.20000000.plumed.dat
Originally used with PLUMED version: 2.5b
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

#cleft_dist
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4 LABELa label for the action so that its output can be referenced in the input to other actions=cleft_distThe DISTANCE action with label cleft_dist calculates the following quantities:
 Quantity   
 Type   
 Description  
cleft_dist
scalar
the DISTANCE between this pair of atoms
TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=2,1,3,4 LABELa label for the action so that its output can be referenced in the input to other actions=dihedralThe TORSION action with label dihedral calculates the following quantities:
 Quantity   
 Type   
 Description  
dihedral
scalar
the TORSION involving these atoms

dcnThe COMBINE action with label dcn calculates the following quantities:
 Quantity   
 Type   
 Description  
dcn
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=dihedral POWERS the powers to which you are raising each of the arguments in your function=1 COEFFICIENTS the coefficients of the arguments in your function=-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dc2The COMBINE action with label dc2 calculates the following quantities:
 Quantity   
 Type   
 Description  
dc2
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=dihedral POWERS the powers to which you are raising each of the arguments in your function=2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#bias mean and variance
edsThe EDS action with label eds calculates the following quantities:
 Quantity   
 Type   
 Description  
eds.bias
scalar
the instantaneous value of the bias potential
eds.force2
scalar
squared value of force from the bias
eds.dcn_coupling
scalar
For each named CV biased, there will be a corresponding output CV_coupling storing the current linear bias prefactor. This particular component measures this quantity for the input CV named dcn: EDSAdd a linear bias on a set of observables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=dcn CENTERThe desired centers (equilibrium values) which will be sought during the adaptive linear biasing=0.11 PERIODSteps over which to adjust bias for adaptive or ramping=1000 OUT_RESTARTOutput file for all information needed to continue EDS simulation=gatp-enm-12site_FEStart_eq175ns.range10_init0.10ps.run.20000000.restart.dat  RANGE The (starting) maximum increase in coupling constant per PERIOD (in k_B T/[BIAS_SCALE unit]) for each CV biased=10.0 INIT Starting value for coupling constant=0
eds: EDSAdd a linear bias on a set of observables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=dcn CENTERThe desired centers (equilibrium values) which will be sought during the adaptive linear biasing=0.11 PERIODSteps over which to adjust bias for adaptive or ramping=1000 OUT_RESTARTOutput file for all information needed to continue EDS simulation=gatp-enm-12site_FEStart_eq175ns.range10_init0.10ps.run.20000000.restart.dat  RANGE The (starting) maximum increase in coupling constant per PERIOD (in k_B T/[BIAS_SCALE unit]) for each CV biased=10.0 INIT Starting value for coupling constant=0  FIXED Fixed target values for coupling constant=0 SEED Seed for random order of changing bias=0 LM_MIXING Initial mixing parameter when using Levenberg-Marquadt minimization=1

#write every 100 ps
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cleft_dist,dcn,eds.dcn_coupling,eds.bias,eds.force2 FILEthe name of the file on which to output these quantities=gatp-enm-12site_FEStart_eq175ns.range10_init0.10ps.run.20000000.colvars.dat STRIDE the frequency with which the quantities of interest should be output=1000