Project ID: plumID:20.015
Source: 2-EMMI/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr
# uncomment next line if your restart #RESTART # load extra file # set to correct location LOAD FILE=EMMIVox.cpp # include topology info - set path a PDB file MOLINFO STRUCTURE=../0-TOPO/step5_charmm2gmx.pdb # define all heavy atoms - set path to index file protein-h: GROUP NDX_FILE=../0-TOPO/index.ndx NDX_GROUP=PROT-H # make protein whole and in the cell where map is defined WHOLEMOLECULES ... ADDREFERENCE ENTITY0=1-6701 REF0=5.3607,4.5911,3.1497 ENTITY1=6702-6741 REF1=3.2439,3.3684,6.0308 ... WHOLEMOLECULES # create EMMI score EMMIVOX ... # name of this action LABEL=gmm # general parameters - do not change this! TEMP=303.15 NL_STRIDE=50 NL_CUTOFF=0.5 NS_CUTOFF=1.0 # define atoms for cryo-EM restraint and read experimental data # set path to map file if not in current directory ATOMS=protein-h DATA_FILE=map_zoned_align.dat # info about the experimental map NORM_DENSITY=2068.185 RESOLUTION=0.1 VOXEL=0.1012 # data likelihood (or noise model): Marginal NOISETYPE=MARGINAL SIGMA_MIN=0.2 # write output STATUS_FILE=EMMIStatus WRITE_STRIDE=2500 ... # translate into bias - updated every 2 time steps emr: BIASVALUE ARG=gmm.scoreb STRIDE=2 # print output to file PRINT ARG=gmm.* FILE=COLVAR STRIDE=2500