Project ID: plumID:21.042
Source: Plumed_nest/plumed_Nce6Ncp6_Au111.dat
Originally used with PLUMED version: 2.4
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

## RESTART

MOLINFO MOLTYPE=protein STRUCTURE=Nce6Ncp6.pdb

## ENERGY LABEL=energy

bb: COM ATOMS=7201,7203,7206,7225,7226,7229,7248,7249,7252,7271,7272,7275,7294,7295,7298,7317,7318,7321,7340,7341,7344,7355,7356,7359,7370,7371,7374,7385,7386,7389,7400,7401,7404,7415,7416,7419
pr1: COM ATOMS=7211,7214-7224
pr2: COM ATOMS=7234,7237-7247
pr3: COM ATOMS=7257,7260-7270
pr4: COM ATOMS=7280,7283-7293
pr5: COM ATOMS=7303,7306-7316
pr6: COM ATOMS=7326,7329-7339
cc1: COM ATOMS=7346-7354
cc2: COM ATOMS=7361-7369
cc3: COM ATOMS=7376-7384
cc4: COM ATOMS=7391-7399
cc5: COM ATOMS=7406-7414
cc6: COM ATOMS=7421-7429

## com: COM ATOMS=7201-7432

dbb: DISTANCE ATOMS=7200,bb COMPONENTS NOPBC
dpr1: DISTANCE ATOMS=7200,pr1 COMPONENTS NOPBC
dpr2: DISTANCE ATOMS=7200,pr2 COMPONENTS NOPBC
dpr3: DISTANCE ATOMS=7200,pr3 COMPONENTS NOPBC
dpr4: DISTANCE ATOMS=7200,pr4 COMPONENTS NOPBC
dpr5: DISTANCE ATOMS=7200,pr5 COMPONENTS NOPBC
dpr6: DISTANCE ATOMS=7200,pr6 COMPONENTS NOPBC
dcc1: DISTANCE ATOMS=7200,cc1 COMPONENTS NOPBC
dcc2: DISTANCE ATOMS=7200,cc2 COMPONENTS NOPBC
dcc3: DISTANCE ATOMS=7200,cc3 COMPONENTS NOPBC
dcc4: DISTANCE ATOMS=7200,cc4 COMPONENTS NOPBC
dcc5: DISTANCE ATOMS=7200,cc5 COMPONENTS NOPBC
dcc6: DISTANCE ATOMS=7200,cc6 COMPONENTS NOPBC

## dcom: DISTANCE ATOMS=7200,com COMPONENTS NOPBC

UPPER_WALLS ARG=dbb.z AT=8.0 KAPPA=1000000 LABEL=uwall_dbb
UPPER_WALLS ARG=dpr1.z AT=8.0 KAPPA=1000000 LABEL=uwall_dpr1
UPPER_WALLS ARG=dpr2.z AT=8.0 KAPPA=1000000 LABEL=uwall_dpr2
UPPER_WALLS ARG=dpr3.z AT=8.0 KAPPA=1000000 LABEL=uwall_dpr3
UPPER_WALLS ARG=dpr4.z AT=8.0 KAPPA=1000000 LABEL=uwall_dpr4
UPPER_WALLS ARG=dpr5.z AT=8.0 KAPPA=1000000 LABEL=uwall_dpr5
UPPER_WALLS ARG=dpr6.z AT=8.0 KAPPA=1000000 LABEL=uwall_dpr6
UPPER_WALLS ARG=dcc1.z AT=8.0 KAPPA=1000000 LABEL=uwall_dcc1
UPPER_WALLS ARG=dcc2.z AT=8.0 KAPPA=1000000 LABEL=uwall_dcc2
UPPER_WALLS ARG=dcc3.z AT=8.0 KAPPA=1000000 LABEL=uwall_dcc3
UPPER_WALLS ARG=dcc4.z AT=8.0 KAPPA=1000000 LABEL=uwall_dcc4
UPPER_WALLS ARG=dcc5.z AT=8.0 KAPPA=1000000 LABEL=uwall_dcc5
UPPER_WALLS ARG=dcc6.z AT=8.0 KAPPA=1000000 LABEL=uwall_dcc6


GYRATION TYPE=RADIUS ATOMS=7201-7432 LABEL=rg

PBMETAD ...
WALKERS_MPI
ARG=dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,dcc4.z,dcc5.z,dcc6.z,rg
SIGMA=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02
HEIGHT=1.2 #kJ/mol
PACE=500
BIASFACTOR=20
TEMP=298.0
LABEL=PBMETAD
GRID_MIN=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
GRID_MAX=8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,7
FILE=HILLS.dbb,HILLS.dpr1,HILLS.dpr2,HILLS.dpr3,HILLS.dpr4,HILLS.dpr5,HILLS.dpr6,HILLS.dcc1,HILLS.dcc2,HILLS.dcc3,HILLS.dcc4,HILLS.dcc5,HILLS.dcc6,HILLS.rg
... PBMETAD

PRINT ARG=PBMETAD.bias,dbb.z,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,dcc4.z,dcc5.z,dcc6.z,rg STRIDE=500 FILE=COLVAR