Project ID: plumID:23.041
Source: 03-7n00/2-Production/cc-1.0/plumed_EMMI.dat
Originally used with PLUMED version: 2.10
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# if you are restarting the run, please uncomment this line #RESTART # include topology infoMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=../../1-Data/step3_input_xtc.pdba file in pdb format containing a reference structureWHOLE# define map atoms system-map:The reference structure is whole, iGROUPDefine 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 detailsNDX_FILE=../../1-Data/index.ndxthe name of index file (gromacs syntax)NDX_GROUP=System-MAP # make map atoms wholethe name of the group to be imported (gromacs syntax) - first group found is used by defaultWHOLEMOLECULES...This action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsADDREFERENCEDefine the reference position of the first atom of each entity using a PDB fileEMSTDefine atoms sequence in entities using an Euclidean minimum spanning treeENTITY0=system-mapthe atoms that make up a molecule that you wish to alignSTRIDE=4 ... WHOLEMOLECULESthe frequency with which molecules are reassembled
# create EMMI scoreEMMIVOX... # name of this actionBayesian single-structure and ensemble refinement with cryo-EM maps. More detailsLABEL=emmi # general parameters - do not change this! # NL_STRIDE: update neighbor list stride # NL_DIST_CUTOFF: distance cutoff in nm # NL_GAUSS_CUTOFF: cutoff based on the Gaussian sigmaa label for the action so that its output can be referenced in the input to other actionsTEMP=300.0temperatureNL_STRIDE=50neighbor list update frequencyNL_DIST_CUTOFF=1.0neighbor list distance cutoffNL_GAUSS_CUTOFF=3.0 # define atoms for cryo-EM restraint and read experimental dataneighbor list Gaussian sigma cutoffATOMS=system-mapatoms used in the calculation of the density map, typically all heavy atomsDATA_FILE=emd_plumed_aligned.dat # info about the experimental mapfile with cryo-EM mapNORM_DENSITY=849.378845integral of experimental densityRESOLUTION=0.227 # data likelihood (or noise model): Marginalcryo-EM map resolutionSIGMA_MIN=0.2minimum density errorGPU# output: in production write with the frequency at which XTC/TRR are writtencalculate EMMIVOX on GPU with LibtorchSTATUS_FILE=EMMIStatuswrite a file with all the data useful for restartWRITE_STRIDE=5000 # comment this if you have a hetero-complex #BFACT_NOCHAIN # in production, you should sample Bfactorsstride for writing status fileDBFACT=0.05Bfactor MC stepMCBFACT_STRIDE=500Bfactor MC strideBFACT_SIGMA=0.1 # scale factorBfactor sigma priorSCALE=1.350000 # correlationscale factorCORRELATION...calculate correlation coefficient
# in production, apply bias to system # translate into bias - updated every 2/4 time steps # emr: BIASVALUE ARG=emmi.scoreb STRIDE=2 emr:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=emmi.scorebthe input for this action is the scalar output from one or more other actionsSTRIDE=4 # # print output to filethe frequency with which the forces due to the bias should be calculatedPrint quantities to a file. More detailsARG=emmithe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be output