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_init0.25ps.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
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,4 
LABEL
a 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
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=2,1,3,4 
LABEL
a 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: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the 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 
PERIODIC
if 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: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=dihedral 
POWERS
 the powers to which you are raising each of the arguments in your function
=2 
PERIODIC
if 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: 
EDS
Add a linear bias on a set of observables. This action has hidden defaults. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dcn 
CENTER
The desired centers (equilibrium values) which will be sought during the adaptive linear biasing
=0.11 
PERIOD
Steps over which to adjust bias for adaptive or ramping
=2500 
OUT_RESTART
Output file for all information needed to continue EDS simulation
=gatp-enm-12site_FEStart_eq175ns.range10_init0.25ps.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: 
EDS
Add a linear bias on a set of observables. This action uses the defaults shown here. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dcn 
CENTER
The desired centers (equilibrium values) which will be sought during the adaptive linear biasing
=0.11 
PERIOD
Steps over which to adjust bias for adaptive or ramping
=2500 
OUT_RESTART
Output file for all information needed to continue EDS simulation
=gatp-enm-12site_FEStart_eq175ns.range10_init0.25ps.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
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cleft_dist,dcn,eds.dcn_coupling,eds.bias,eds.force2 
FILE
the name of the file on which to output these quantities
=gatp-enm-12site_FEStart_eq175ns.range10_init0.25ps.run.20000000.colvars.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000