Project ID: plumID:21.039
Source: data/chignolin/1_opes_multi/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
#################################### # >> Chignolin << # OPES Multicanonical simulation ####################################
#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.htmlMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=chignolin-ref.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-166the atoms that make up a molecule that you wish to align
# Define CVs
# Select Calpha PROTEIN: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=1-166 CA:the numerical indexes for the set of atoms in the groupGROUPDefine 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=5,26,47,61,73,88,102,109,123,147 # RMSD rmsd_ca:the numerical indexes for the set of atoms in the groupRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=chignolin-ca.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL # END-TO-END DISTANCE end:the manner in which RMSD alignment is performedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,147 # HBONDS hbonds:the pair of atom that we are calculating the distance betweenCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=23,145the atoms involved in each of the contacts you wish to calculateATOMS2=45,120the atoms involved in each of the contacts you wish to calculateATOMS3=56,100the atoms involved in each of the contacts you wish to calculateATOMS4=56,107the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.4 NN=6 MM=8}The switching functions to use for each of the contacts in your mapSUMene:calculate the sum of all the contacts in the inputENERGYCalculate the total potential energy of the simulation box. More details
# Define Bias mc:ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. More detailsARG=enethe label of the internal energy of the systemTEMP_MIN=270the minimum of the temperature rangeTEMP_MAX=700 opes:the maximum of the temperature rangeOPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More detailsPACE=500how often the bias is updatedARG=mcthe label of the ECVs that define the expansionWALKERS_MPIswitch on MPI version of multiple walkersPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=5000the frequency with which all the open files should be flushedENDPLUMEDTerminate plumed input. More details