Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV1/plumed.0.dat
Originally used with PLUMED version: 2.5.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTARTMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=Protein.pdba file in pdb format containing a reference structureMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-709the atoms that make up a molecule that you wish to alignRANDOM_EXCHANGESSet random pattern for exchanges. More details
ca: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 detailsATOMS=5,12,23,42,56,70,84,104,118,132,146,160,174,185,199,213,225,244,256,280,292,316,338,352,362,381,395,416,428,450,472,484,498,524,536,553,567,579,591,607,626,640,654,676,683,697 cv1:the numerical indexes for the set of atoms in the groupCOORDINATIONCalculate coordination numbers. More detailsGROUPA=caFirst list of atomsNN=8The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NNR_0=0.65The r_0 parameter of the switching functionNOPBCignore the periodic boundary conditions when calculating distancesNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=5.0The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor list
uwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cv1the arguments on which the bias is actingAT=350.0the positions of the wallKAPPA=30.0 lwall:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=cv1the arguments on which the bias is actingAT=150.0the positions of the wallKAPPA=30.0the force constant for the wall
metad:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=cv1the input for this action is the scalar output from one or more other actionsPACE=2500the frequency for hill additionHEIGHT=0.3the heights of the Gaussian hillsSIGMA=2.0the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=500.0the upper bounds for the gridGRID_SPACING=0.25the approximate grid spacing (to be used as an alternative or together with GRID_BIN)Print quantities to a file. More detailsSTRIDE=10the frequency with which the quantities of interest should be outputARG=cv1,metad.bias,uwall.bias,lwall.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVAR #PRINT STRIDE=10 ARG=cv1,metad.bias FILE=COLVARthe name of the file on which to output these quantities