Project ID: plumID:19.007
Source: EMMI-MT/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr
# include topology info: this is needed to identify atom types MOLINFO STRUCTURE=structure.pdb # define all heavy atoms using GROMACS index file # which can be created with gmx_mpi make_ndx protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H protein: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein protein-no-negative: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-no-negative-no-h # make protein whole: add reference position of first heavy atom (in nm) WHOLEMOLECULES ADDREFERENCE ENTITY0=protein REF0=3.217,4.340,6.195 # create EMMI score EMMI ... LABEL=gmm NOPBC TEMP=300.0 NL_STRIDE=50 NL_CUTOFF=0.01 ATOMS=protein-no-negative GMM_FILE=AC_SYMM.dat #ATOMS selects what is refined # no-negative-no-h or no-h are reasonable # resolution is not used - no Bfactor fitting # SIGMA_MIN can go down to 0.02, must be > NL_CUTOFF, # if crashes, raise back to 0.05, # the larger the number the softer the contribution of the EM data SIGMA_MIN=0.05 RESOLUTION=0.1 NOISETYPE=MARGINAL ... # translate into bias emr: BIASVALUE ARG=gmm.scoreb STRIDE=2 # print useful info to file PRINT ARG=gmm.* FILE=COLVAR STRIDE=500