PLUMED-NEST

Project ID: plumID:22.036
Source: plumed.dat
Originally used with PLUMED version: 2.5.6
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
# PDB that provides information on the molecules that are present in your system.
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=./GHBFIX.cpp

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=ref.pdb
#WHOLEMOLECULES ENTITY0=1-2026
# Flush open files regularly in case of data loss
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000

#eRMSD_start: ...
#  ERMSD
#  ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64
#  REFERENCE=ref.pdb
#...


####################################################################################################
# gHBfix RESTRAINT SECTION
####################################################################################################

# GroupA and GroupB are all relevant donors and acceptors. D_0, D_MAX and C have to be defined according to the gHBfix switching function - default values printed (Kuehrova, Mlynsky et al., JCTC 2019). Each relevant type of donor and acceptor are labeled with an integer (typesTable.dat) and eta/scaling parameters are specified (scalingParameters.dat).
group_1: 
GHBFIX
Calculate the GHBFIX interaction energy among GROUPA and GROUPB More details
 
PAIR
 Pair only 1st element of the 1st group with 1st element in the second, etc
 
GROUPA
First list of atoms
=20,18,494,492,1036,1034,1503,1505,1508,240,242,244,274,272,1252,1254,1257,1288,1286 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1007,1005,1540,1538,2017,2015,523,525,527,779,781,784,1760,1758,1790,1792,1794,752,750 
D_0
the value of D_0 in the switching function
=0.23 
D_MAX
the value of D_MAX in the switching function
=0.33 
C
the value of C in the switching function
=0.8 
TYPES
the value of TYPES in the switching function
=typesTable.dat 
PARAMS
the value of PARAMS in the switching function
=scalingParameters.dat

The GHBFIX action with label group_1 calculates a scalar quantitytot_1: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=group_1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 

The COMBINE action with label tot_1 calculates a scalar quantity
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=tot_1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=all_1



# Coordination number within middle base pairs as a CV
The BIASVALUE action with label all_1 calculates the following quantities:
 Quantity   
 Description  
all_1.bias
the instantaneous value of the bias potential
all_1._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filebp8_25: 
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
=233-244,773-787
bp9_56: 
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
=263-276,1751-1764
bp24_41: 
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
=741-754,1279-1292
bp57_40: 
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
=1246-1260,1783-1794

h12: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=bp8_25 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=bp9_56 
R_0
The r_0 parameter of the switching function
=0.3 
NN
 The n parameter of the switching function 
=4
The COORDINATION action with label h12 calculates a scalar quantityh34: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=bp24_41 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=bp57_40 
R_0
The r_0 parameter of the switching function
=0.3 
NN
 The n parameter of the switching function 
=4
The COORDINATION action with label h34 calculates a scalar quantityh13: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=bp8_25 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=bp24_41 
R_0
The r_0 parameter of the switching function
=0.3 
NN
 The n parameter of the switching function 
=4
The COORDINATION action with label h13 calculates a scalar quantityh24: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=bp9_56 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=bp57_40 
R_0
The r_0 parameter of the switching function
=0.3 
NN
 The n parameter of the switching function 
=4

# Function to CVs that unifies the Gaussian width
The COORDINATION action with label h24 calculates a scalar quantitys12: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
ARG
the input for this action is the scalar output from one or more other actions
=h12 
FUNC
the function you wish to evaluate
=x^0.65 
The CUSTOM action with label s12 calculates a scalar quantitys34: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
ARG
the input for this action is the scalar output from one or more other actions
=h34 
FUNC
the function you wish to evaluate
=x^0.65
#s13: CUSTOM PERIODIC=NO ARG=h13 FUNC=x^0.65
#s24: CUSTOM PERIODIC=NO ARG=h24 FUNC=x^0.65

#isoi: CUSTOM ARG=s12,s34 FUNC=x+y PERIODIC=NO
#isoi_1: CUSTOM ARG=s12,s34 FUNC=x-y PERIODIC=NO

# Set wall to restraint CV space
#LOWER_WALLS ARG=isoi_1 AT=0 KAPPA=0.22 LABEL=lwall
The CUSTOM action with label s34 calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=h13,h24 
AT
the positions of the wall
=10,10 
KAPPA
the force constant for the wall
=0.02,0.02 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall

# Well-tempered MetaDynamics
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialmetad: ...
  
METAD
Used to performed metadynamics on one or more collective variables. More details
  
ARG
the input for this action is the scalar output from one or more other actions
=s12,s34
  
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=2.5 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15
  
SIGMA
the widths of the Gaussian hills
=0.8,0.8
  
FILE
 a file in which the list of added hills is stored
=HILLS 
GRID_MIN
the lower bounds for the grid
=0,0 
GRID_MAX
the upper bounds for the grid
=26,26
  
GRID_WSTRIDE
write the grid to a file every N steps
=25000000 
GRID_WFILE
the file on which to write the grid
=GRID 
GRID_RFILE
a grid file from which the bias should be read at the initial step of the simulation
=GRID
...

#DEBUG DETAILED_TIMERS

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=h12,h34,s12,s34,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=tot_1,all_1.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=2500 
FILE
the name of the file on which to output these quantities
=check_gHBfix_one-zero.dat