Project ID: plumID:22.029
Source: metad.dat
Originally used with PLUMED version: 2.5
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
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# RESTART append output files of several restarts 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=1-85 #groups ang_noh: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index_meta2.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=ang_noh waters_noh: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index_meta2.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=ang_noh donors: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index_meta2.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=donors acceptors: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index_meta2.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=acceptors #gyration radius GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-85 LABELa label for the action so that its output can be referenced in the input to other actions=rg
#walls uw: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg KAPPAthe force constant for the wall=10000 ATthe positions of the wall=0.85 lw: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rg KAPPAthe force constant for the wall=10000 ATthe positions of the wall=0.5 # Coordination number c: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=ang_noh GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=waters_noh R_0The r_0 parameter of the switching function=0.35 hbs: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=donors GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=acceptors R_0The r_0 parameter of the switching function=0.25
# Metadynamics METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... ARGthe labels of the scalars on which the bias will act=rg,hbs GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=1,56 SIGMAthe widths of the Gaussian hills=0.1,0.1 HEIGHTthe heights of the Gaussian hills=1.2 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300. LABELa 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rg FILEthe name of the file on which to output these quantities=rg.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=metad.* FILEthe 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 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c FILEthe 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 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=hbs FILEthe name of the file on which to output these quantities=all_coordination_25.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rg,hbs,metad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=lw.*,uw.* FILEthe name of the file on which to output these quantities=restraint.dat STRIDE the frequency with which the quantities of interest should be output=500 FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500