Project ID: plumID:20.014
Source: PLUMED_input_files/AB42_and_10074_G5/plumed/plumed.dat
Originally used with PLUMED version: 2.6.0
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

#this is the master plumed.dat file for metadynamic metainference simulations

# define groups
MOLINFO STRUCTURE=../system/template.pdb
WHOLEMOLECULES ENTITY0=1-627 ENTITY1=628-664
FLUSH STRIDE=1000

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

#include file with definition of metadynamics CVs involving the small molecule
INCLUDE FILE=CVs_drug.dat

# Chemical shifts at 278 K
cs: CS2BACKBONE ATOMS=1-627 DATADIR=../data NOPBC TEMPLATE=../system/template.pdb

#activate parallel bias metadynamics
PBMETAD ...
ARG=helix.lessthan,beta,rgyr,hydro,salt,dihcor,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4
    HEIGHT=1.2
    BIASFACTOR=49 #10*SQRT(NUM_OF_CVS)
    SIGMA=0.64,0.33,0.03,0.69,2.75,1.34,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.1,0.1,0.1,0.1
    PACE=500
    GRID_MIN=-1,-1,-1,-1,-1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-pi,-pi,-pi,-pi
    GRID_MAX=100,100,20,200,400,50,150,150,150,150,150,150,150,150,150,150,150,150,150,150,pi,pi,pi,pi
    GRID_SPACING=0.1,0.1,0.01,0.1,0.1,0.01,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.01,0.01,0.01,0.01    
    GRID_WSTRIDE=10000
    #GRID_RFILES=GRID.helix.lessthan,GRID.beta,GRID.rgyr,GRID.hydro,GRID.salt,GRID.dihcor,GRID.reg1,GRID.reg2,GRID.reg3,GRID.reg4,GRID.reg5,GRID.reg6,GRID.reg7,GRID.reg8,GRID.reg9,GRID.reg10,GRID.reg11,GRID.reg12,GRID.reg13,GRID.reg14,GRID.ligtor1,GRID.ligtor2,GRID.ligtor3,GRID.ligtor4
    FILE=HILLS_helix,HILLS_beta,HILLS_rgyr,HILLS_hydro,HILLS_salt,HILLS_dihcor,HILLS_reg1,HILLS_reg2,HILLS_reg3,HILLS_reg4,HILLS_reg5,HILLS_reg6,HILLS_reg7,HILLS_reg8,HILLS_reg9,HILLS_reg10,HILLS_reg11,HILLS_reg12,HILLS_reg13,HILLS_reg14,HILLS_ligtor1,HILLS_ligtor2,HILLS_ligtor3,HILLS_ligtor4
    WALKERS_MPI
    LABEL=pbmetad
... PBMETAD

# Metainference - one sigma per nucleus
cs_ha: METAINFERENCE ARG=(cs\.ha-.*),pbmetad.bias PARARG=(cs\.expha-.*) SIGMA0=9.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.1 NOISETYPE=GAUSS REWEIGHT SIGMA_MEAN0=0.5 OPTSIGMAMEAN=SEM AVERAGING=500 WRITE_STRIDE=2500 STATUS_FILE=MISTATUS.cs_ha
cs_hn: METAINFERENCE ARG=(cs\.hn-.*),pbmetad.bias PARARG=(cs\.exphn-.*) SIGMA0=9.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.1 NOISETYPE=GAUSS REWEIGHT SIGMA_MEAN0=0.5 OPTSIGMAMEAN=SEM AVERAGING=500 WRITE_STRIDE=2500 STATUS_FILE=MISTATUS.cs_hn
cs_nh: METAINFERENCE ARG=(cs\.nh-.*),pbmetad.bias PARARG=(cs\.expnh-.*) SIGMA0=9.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.1 NOISETYPE=GAUSS REWEIGHT SIGMA_MEAN0=0.5 OPTSIGMAMEAN=SEM AVERAGING=500 WRITE_STRIDE=2500 STATUS_FILE=MISTATUS.cs_nh
cs_ca: METAINFERENCE ARG=(cs\.ca-.*),pbmetad.bias PARARG=(cs\.expca-.*) SIGMA0=9.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.1 NOISETYPE=GAUSS REWEIGHT SIGMA_MEAN0=0.5 OPTSIGMAMEAN=SEM AVERAGING=500 WRITE_STRIDE=2500 STATUS_FILE=MISTATUS.cs_ca
cs_cb: METAINFERENCE ARG=(cs\.cb-.*),pbmetad.bias PARARG=(cs\.expcb-.*) SIGMA0=9.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.1 NOISETYPE=GAUSS REWEIGHT SIGMA_MEAN0=0.5 OPTSIGMAMEAN=SEM AVERAGING=500 WRITE_STRIDE=2500 STATUS_FILE=MISTATUS.cs_cb
cs_co: METAINFERENCE ARG=(cs\.co-.*),pbmetad.bias PARARG=(cs\.expco-.*) SIGMA0=9.0 SIGMA_MIN=0.00001 SIGMA_MAX=10.0 DSIGMA=0.1 NOISETYPE=GAUSS REWEIGHT SIGMA_MEAN0=0.5 OPTSIGMAMEAN=SEM AVERAGING=500 WRITE_STRIDE=2500 STATUS_FILE=MISTATUS.cs_co

# Ensemble statistics
ens: ENSEMBLE ARG=(cs\.ha-.*),(cs\.hn-.*),(cs\.nh-.*),(cs\.ca-.*),(cs\.cb-.*),(cs\.co-.*),pbmetad.bias REWEIGHT

STATS ...
    ARG=(ens\.cs\.ha-.*),(ens\.cs\.hn-.*),(ens\.cs\.nh-.*),(ens\.cs\.ca-.*),(ens\.cs\.cb-.*),(ens\.cs\.co-.*)
    PARARG=(cs\.expha-.*),(cs\.exphn-.*),(cs\.expnh-.*),(cs\.expca-.*),(cs\.expcb-.*),(cs\.expco-.*) 
    LABEL=stat
... STATS

PRINT ARG=helix.lessthan,beta,rgyr,hydro,salt,dihcor,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4,pbmetad.bias FILE=COLVAR STRIDE=500
PRINT ARG=(ens.*),(stat.*) FILE=STATS STRIDE=500
PRINT ARG=(cs_ha.*) FILE=BAYES.HA STRIDE=500
PRINT ARG=(cs_hn.*) FILE=BAYES.HN STRIDE=500
PRINT ARG=(cs_nh.*) FILE=BAYES.NH STRIDE=500
PRINT ARG=(cs_ca.*) FILE=BAYES.CA STRIDE=500
PRINT ARG=(cs_cb.*) FILE=BAYES.CB STRIDE=500
PRINT ARG=(cs_co.*) FILE=BAYES.CO STRIDE=500
ENDPLUMED