PLUMED-NEST

Project ID: plumID:19.021
Source: ./Trajectories/EDS-flattening-enm/us-flatten-dihed-mean/gatp-enm-12site_FEStart_eq175ns.flatten_us_k500/gatp-enm-12site_FEStart_eq175ns.flatten_us_k500.50ps.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

#bias mean 
usThe RESTRAINT action with label us calculates the following quantities:
 Quantity   
 Type   
 Description  
us.bias
scalar
the instantaneous value of the bias potential
us.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details
 
ARG
the arguments on which the bias is acting
=dcn 
AT
the position of the restraint
=0.110262 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=500
us: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details
 
ARG
the arguments on which the bias is acting
=dcn 
AT
the position of the restraint
=0.110262 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=500  
SLOPE
 specifies that the restraint is linear and what the values of the force constants on each of the variables are
=0.0

#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,us.bias,us.force2 
FILE
the name of the file on which to output these quantities
=gatp-enm-12site_FEStart_eq175ns.flatten_us_k500.50ps.run.20000000.colvars.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1000