Project ID: plumID:19.005
Source: cmyc_and_10058_F4/plumed/plumed_master.dat
Originally used with PLUMED version: 2.5
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

#this is the master_plumed.dat file for metainference metadynamics simulations

# define groups
MOLINFO STRUCTURE=../system/template.pdb
prot: GROUP ATOMS=1-191
drug: GROUP ATOMS=192-218
first: GROUP ATOMS=1-76
second: GROUP ATOMS=77-119
third: GROUP ATOMS=120-191
WHOLEMOLECULES ENTITY0=prot ENTITY1=drug

#include file with definition of metadynamics CVs
INCLUDE FILE=meta_cv_plumed.dat

#activate parallel bias metadynamics 
PBMETAD ... #activating start
LABEL=pbmetad #to print out things
ARG=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,fstdr,scddr,trddr
PACE=500 HEIGHT=1.2 BIASFACTOR=10 WALKERS_MPI
SIGMA=1.01,0.89,0.41,0.72,0.05,0.71,0.05,0.05,0.05
FILE=HILLS_ahelixright,HILLS_betasheet,HILLS_ahelixleft,HILLS_polypro,HILLS_rgyr,HILLS_ohbond,HILLS_fstdr,HILLS_scddr,HILLS_trddr
GRID_MIN=-2,-2,-2,-2,0.2,0,0,0,0
GRID_MAX=20,20,20,20,1.4,30,5.2,5.2,5.2
#actual min and max are slightly different, but allowing for gaussian distribution around it
... PBMETAD

#include file with definition of experimental CVs
INCLUDE FILE=exp_cv_plumed.dat

# metainference stuff
mi_cs_ha: METAINFERENCE ARG=(cs\.ha_.*),pbmetad.bias PARARG=(cs\.expha_.*) REWEIGHT NOISETYPE=GAUSS SIGMA0=1.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.5 SIGMA_MEAN0=0.645 
mi_cs_ca: METAINFERENCE ARG=(cs\.ca_.*),pbmetad.bias PARARG=(cs\.expca_.*) REWEIGHT NOISETYPE=GAUSS SIGMA0=1.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.5 SIGMA_MEAN0=0.645 
mi_cs_cb: METAINFERENCE ARG=(cs\.cb_.*),pbmetad.bias PARARG=(cs\.expcb_.*) REWEIGHT NOISETYPE=GAUSS SIGMA0=1.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.5 SIGMA_MEAN0=0.645 

#print out relavant info
PRINT STRIDE=200 ARG=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,fstdr,scddr,trddr,pbmetad.bias FILE=COLVAR_PBMETAD
PRINT STRIDE=200 ARG=mi_cs_ha.*,mi_cs_ca.*,mi_cs_cb.* FILE=COLVAR_MI