Project ID: plumID:20.028
Source: wild-type/plumed-1.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More detailsFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsREFERENCE=step5_charmm2gmx-modified-1.pdb first:a file in pdb format containing the reference structure and the atoms involved in the CVCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=3006-3053 # GTP second:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=2955-3005 # FAR last:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=9733-33193:138 # all P atoms in system--range with a stride 118 gtp:the group of atoms that you are calculating the Gyration Tensor forDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=first,lastthe pair of atom that we are calculating the distance betweenCOMPONENTSfar:calculate the x, y and z components of the distance separately and store them as labelDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=second,lastthe pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as label
# Activate metadynamics in phi and psi # depositing a Gaussian every 500 time steps, # with height equal to 1.2 kJoule/mol, # and width 0.35 rad for both CVs.METAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=gtp.z,far.zthe input for this action is the scalar output from one or more other actionsPACE=500the frequency for hill additionHEIGHT=1.2the heights of the Gaussian hillsSIGMA=0.10,0.35the widths of the Gaussian hillsFILE=HILLS2a file in which the list of added hills is storedBIASFACTOR=5.0use well tempered metadynamics and use this bias factorTEMP=310.0the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-15.0,-10.0the lower bounds for the gridGRID_MAX=15.0,10.0 ... METADthe upper bounds for the grid
# monitor the two variables and the metadynamics bias potentialPrint quantities to a file. More detailsSTRIDE=200the frequency with which the quantities of interest should be outputARG=gtp.z,far.z,metad.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVAR2the name of the file on which to output these quantities