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 WHOLEMOLECULESThis 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 e0: 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_H.pdb e3: 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 ee3: 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 r0: RMSDCalculate the RMSD with respect to a reference structure. 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 r3: RMSDCalculate the RMSD with respect to a reference structure. 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 metad: 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