PLUMED-NEST

Project ID: plumID:19.009
Source: UUCG/ccUUCGgg.plumed.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

# RESTART
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
=UUCG_8_L.pdb
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
=1-254

e0: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=UUCG_8_H.pdb
The ERMSD action with label e0 calculates a scalar quantitye3: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=UUCG_8_L.pdb

The ERMSD action with label e3 calculates a scalar quantityee3: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=UUCG_8_L.pdb 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=3.2

The ERMSD action with label ee3 calculates a scalar quantityr0: 
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
=UUCG_8_H.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
r3: 
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
=UUCG_8_L.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL


metad: 
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
=ee3 
PACE
the frequency for hill addition
=500000001 
HEIGHT
the heights of the Gaussian hills
=0.0 
SIGMA
the widths of the Gaussian hills
=0.1 
FILE
 a file in which the list of added hills is stored
=HILLS_avg_5 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.882 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
GRID_MIN
the lower bounds for the grid
=0.0 
GRID_MAX
the upper bounds for the grid
=5.0 
GRID_BIN
the number of bins for the grid
=250

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
=e3,ee3,e0,r3,r0,metad.bias 
FILE
the name of the file on which to output these quantities
=colvar_5 
STRIDE
 the frequency with which the quantities of interest should be output
=1

ENDPLUMED
Terminate plumed input. More details


# histograms below are computed using PLUMED 2.3 syntax

HISTOGRAM ...
REWEIGHT_BIAS
ARG=e3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=3
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0075
GRID_WFILE=fes_ermsd_5_0
UPDATE_FROM=200000
UPDATE_UNTIL=400000
... HISTOGRAM

HISTOGRAM ...
REWEIGHT_BIAS
ARG=e3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=3
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0075
GRID_WFILE=fes_ermsd_5_1
UPDATE_FROM=400000
UPDATE_UNTIL=600000
... HISTOGRAM


HISTOGRAM ...
REWEIGHT_BIAS
ARG=e3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=3
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0075
GRID_WFILE=fes_ermsd_5_2
UPDATE_FROM=600000
UPDATE_UNTIL=800000
... HISTOGRAM


HISTOGRAM ...
REWEIGHT_BIAS
ARG=e3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=3
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0075
GRID_WFILE=fes_ermsd_5_3
UPDATE_FROM=800000
UPDATE_UNTIL=1000000
... HISTOGRAM

ENDPLUMED
################################

HISTOGRAM ...
REWEIGHT_BIAS
ARG=r3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=1
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0025
GRID_WFILE=fes_rmsd_5_0
UPDATE_FROM=0
UPDATE_UNTIL=250000
... HISTOGRAM

HISTOGRAM ...
REWEIGHT_BIAS
ARG=r3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=1
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0025
GRID_WFILE=fes_rmsd_5_1
UPDATE_FROM=250000
UPDATE_UNTIL=500000
... HISTOGRAM


HISTOGRAM ...
REWEIGHT_BIAS
ARG=r3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=1
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0025
GRID_WFILE=fes_rmsd_5_2
UPDATE_FROM=500000
UPDATE_UNTIL=750000
... HISTOGRAM


HISTOGRAM ...
REWEIGHT_BIAS
ARG=r3
TEMP=300.882
USE_ALL_DATA
UNNORMALIZED
GRID_MIN=0
GRID_MAX=1
GRID_BIN=250
RESTART=NO
BANDWIDTH=0.0025
GRID_WFILE=fes_rmsd_5_3
UPDATE_FROM=750000
UPDATE_UNTIL=1000000
... HISTOGRAM