PLUMED-NEST

Project ID: plumID:23.025
Source: repulsive/3ibk/terra_repulsive.dat
Originally used with PLUMED version: 2.7
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

RESTART
Activate restart. More details
The RESTART action with label  calculates something
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A # modify the default length unit (nm) to Angstrom

# TERRA GQ
#########################################
# PDB NUMBERING MUST BE USED HERE
# K1 = 1517 (pdb numbering)
# K2 = 1519 (pdb numbering)
# Kbulk = 35596-35655 (remove drude particles from list!) (pdb numbering)
#########################################

#########################################
# Defining groups and lower_walls
K1: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1517
The GROUP action with label K1 calculates somethingK2: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1519
The GROUP action with label K2 calculates somethingKBULK: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=35596,35598,35600,35602,35604,35606,35608,35610,35612,35614,35616,35618,35620,35622,35624,35626,35628,35630,35632,35634,35636,35638,35640,35642,35644,35646,35648,35650,35652,35654


The GROUP action with label KBULK calculates somethingd1: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K1 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=KBULK 
LOWEST
 this flag allows you to recover the lowest of these variables
The DISTANCES action with label d1 calculates somethingd2: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K2 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=KBULK 
LOWEST
 this flag allows you to recover the lowest of these variables
The DISTANCES action with label d2 calculates somethingd3: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K1 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=K2 
LOWEST
 this flag allows you to recover the lowest of these variables

The DISTANCES action with label d3 calculates somethinglwall1: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1.lowest 
AT
the positions of the wall
=5.5 
KAPPA
the force constant for the wall
=2000.0 
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
The LOWER_WALLS action with label lwall1 calculates somethinglwall2: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d2.lowest 
AT
the positions of the wall
=5.5 
KAPPA
the force constant for the wall
=2000.0 
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
#########################################

The LOWER_WALLS action with label lwall2 calculates something
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
ARG
the input for this action is the scalar output from one or more other actions
=d1.lowest,d2.lowest,d3.lowest 
FILE
the name of the file on which to output these quantities
=mindist.dat