PLUMED-NEST

Project ID: plumID:24.008
Source: 5FU/iMetaD_Input/plumed_imetad.dat
Originally used with PLUMED version: 2.4
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

# Reference structure 
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
=../Structure/yCD_5FU.pdb
# Keep molecules whole
The MOLINFO action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-2423 
ENTITY1
the atoms that make up a molecule that you wish to align
=2424-4846 
ENTITY2
the atoms that make up a molecule that you wish to align
=4847-4858 
ENTITY3
the atoms that make up a molecule that you wish to align
=4859-4870
# Fit heavy atoms to template
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../Structure/heavy_atoms.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

# Contactmap of atoms for path CV
f1: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=4850,895 
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=4850,917 
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=4850,1671 
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=4850,2314 
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=4850,2423 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=1.2}

The CONTACTMAP action with label f1 calculates the following quantities:
 Quantity   
 Description  
f1.contact
By not using SUM or CMDIST each contact will be stored in a componentpath2: 
PATH
Path collective variables with a more flexible framework for the distance metric being used. More details
 
REFERENCE
a pdb file containing the set of reference configurations
=outpath.pdb 
TYPE
 the manner in which distances are calculated
=EUCLIDEAN 
GPATH
 calculate the trigonometric path
 
NOSPATH
 do not calculate the spath CV
 
NOZPATH
 do not calculate the zpath CV

# Group definitions
The PATH action with label path2 calculates somethingsph: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../Structure/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=ChainA-H_ZN-ChainA 
The GROUP action with label sph calculates somethingurl: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../Structure/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=UR1_noH
The GROUP action with label url calculates somethinglig: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../Structure/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=UR1
The GROUP action with label lig calculates somethingref: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../Structure/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H_ZN
# Group sys 
The GROUP action with label ref calculates somethingsys: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../Structure/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein_ZN_UR1_UR2

The GROUP action with label sys calculates something
WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=lig 
AROUND
reference atoms
=sph
# Fixed atom
fix: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=-1.101616,-0.678271,0.017793

The FIXEDATOM action with label fix calculates somethingsph_center: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=sph
The COM action with label sph_center calculates somethingurl_center: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=url

The COM action with label url_center calculates somethingdis: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=sph_center,fix

# We are not going to be biasing these coordinates but we can print them for reference 
The DISTANCE action with label dis calculates the following quantities:
 Quantity   
 Description  
dis.value
the DISTANCE between this pair of atomsabs: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=url_center,sph_center 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label abs calculates the following quantities:
 Quantity   
 Description  
abs.x
the x-component of the vector connecting the two atoms
abs.y
the y-component of the vector connecting the two atoms
abs.z
the z-component of the vector connecting the two atoms
abs.value
the DISTANCE between this pair of atomsrho: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=url_center,sph_center
The DISTANCE action with label rho calculates the following quantities:
 Quantity   
 Description  
rho.value
the DISTANCE between this pair of atomsrel_x: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs.z,abs.y 
FUNC
the function you wish to evaluate
=(x-y)/sqrt(2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label rel_x calculates somethingrel_y: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs.x 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label rel_y calculates somethingrel_z: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs.z,abs.y 
FUNC
the function you wish to evaluate
=(x+y)/sqrt(2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The MATHEVAL action with label rel_z calculates somethingtheta: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=rel_z,rho 
FUNC
the function you wish to evaluate
=acos(x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=0.,pi
The MATHEVAL action with label theta calculates somethingphi: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=rel_x,rel_y 
FUNC
the function you wish to evaluate
=atan2(y,x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-pi,pi

The MATHEVAL action with label phi calculates somethingrmsd: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../Structure/heavy_atoms_5FU1.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

# The restraint on the rmsd
The RMSD action with label rmsd calculates somethingrestr2: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rmsd 
AT
the positions of the wall
=0.1 
KAPPA
the force constant for the wall
=200

# Coordination number just for reference 
The UPPER_WALLS action with label restr2 calculates somethingc: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=url 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=sph 
R_0
The r_0 parameter of the switching function
=0.45

# For the second CV we need the atoms in the pocket
The COORDINATION action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the value of the coordination
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=groups.dat 
# The command:
# INCLUDE FILE=groups.dat 
# ensures PLUMED loads the contents of the file called groups.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label groups.dat calculates somethingpocket: 
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
=435,465,718,893,910,917,1268,1296,1315,1334,1340,1379,1669,2312,2371,2383
# --- End of included input --- The GROUP action with label pocket calculates somethingpocket_center: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=pocket 

The COM action with label pocket_center calculates somethingd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=url_center,pocket_center 

## This is a CV for monitoring the unbinding progress 
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomscc: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4847,4855,4852 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=926,927,725,2378,2377,2423 
R_0
The r_0 parameter of the switching function
=1.0 

# Metadynamics
The COORDINATION action with label cc calculates the following quantities:
 Quantity   
 Description  
cc.value
the value of the coordination
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
=path2.gspath,d2        # bias the new CVs 
GRID_MIN
the lower bounds for the grid
=0,0    
GRID_MAX
the upper bounds for the grid
=10,10
SIGMA
the widths of the Gaussian hills
=0.13,0.02    # sigma taken from reference (Karen Palacio-Rodriguez et. al)
HEIGHT
the heights of the Gaussian hills
=1.5          
PACE
the frequency for hill addition
=50000            # change to a large number for infrequent metadynamics
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15       
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

# print everything
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cc,path2.gspath,path2.gzpath,d2,metad 
FILE
the name of the file on which to output these quantities
=metad_data.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500 

# for reference 
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rho,theta,phi 
FILE
the name of the file on which to output these quantities
=rtp_coord.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c 
FILE
the name of the file on which to output these quantities
=all_coordination_45.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rmsd,restr2 
FILE
the name of the file on which to output these quantities
=rmsd_restraint.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500

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
=500

COMMITTOR
Does a committor analysis. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=cc 
STRIDE
 the frequency with which the CVs are analyzed
=5000
BASIN_LL1
List of lower limits for basin #
=-0.01 
BASIN_UL1
List of upper limits for basin #
=0.01
...