PLUMED-NEST

Project ID: plumID:19.009
Source: GAGA/ccGAGAgg.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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=GAGA_8_H.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-263

e0The ERMSD action with label e0 calculates the following quantities:
 Quantity   
 Type   
 Description  
e0
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_H.pdb
e0: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_H.pdb  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
e3The ERMSD action with label e3 calculates the following quantities:
 Quantity   
 Type   
 Description  
e3
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_L.pdb
e3: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_L.pdb  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4

ee3The ERMSD action with label ee3 calculates the following quantities:
 Quantity   
 Type   
 Description  
ee3
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. ,@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. ,@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_L.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2

r0The RMSD action with label r0 calculates the following quantities:
 Quantity   
 Type   
 Description  
r0
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_H.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
r0: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_H.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
r3The RMSD action with label r3 calculates the following quantities:
 Quantity   
 Type   
 Description  
r3
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_L.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
r3: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_8_L.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0


metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=ee3 PACEthe frequency for hill addition=500000001 HEIGHTthe heights of the Gaussian hills=0.0 SIGMAthe widths of the Gaussian hills=0.1 FILE a file in which the list of added hills is stored=HILLS_avg_5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.882 BIASFACTORuse well tempered metadynamics and use this bias factor=15 GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=5.0 GRID_BINthe number of bins for the grid=250

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=e3,ee3,e0,r3,r0,metad.bias FILEthe 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

ENDPLUMEDTerminate 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

################################

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