PLUMED-NEST

Project ID: plumID:19.017
Source: plumed_metad/metad_24ang.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

WHOLEMOLECULES ENTITY0=1-2593 ENTITY1=2594-2605
FIT_TO_TEMPLATE REFERENCE=../input/heavy_atoms.pdb TYPE=OPTIMAL

# Group definition
prot_noh: GROUP NDX_FILE=../input/index.ndx NDX_GROUP=Protein-H
sph: GROUP NDX_FILE=../input/index.ndx NDX_GROUP=sphere
bnz: GROUP NDX_FILE=../input/index.ndx NDX_GROUP=BNZ_noH

WRAPAROUND ATOMS=bnz AROUND=sph

sph_center: COM ATOMS=sph
bnz_center: COM ATOMS=bnz

sph_coord: POSITION ATOM=sph_center NOPBC
bnz_coord: POSITION ATOM=bnz_center NOPBC

abs_x: MATHEVAL ARG=bnz_coord.x,sph_coord.x FUNC=x-y PERIODIC=NO
abs_y: MATHEVAL ARG=bnz_coord.y,sph_coord.y FUNC=x-y PERIODIC=NO
abs_z: MATHEVAL ARG=bnz_coord.z,sph_coord.z FUNC=x-y PERIODIC=NO

rho: MATHEVAL ARG=abs_x,abs_y,abs_z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
theta: MATHEVAL ARG=abs_z,rho FUNC=acos(x/y) PERIODIC=0.,pi
phi: MATHEVAL ARG=abs_x,abs_y FUNC=atan2(y,x) PERIODIC=-pi,pi

# Restraining potential of the sphere
restr: UPPER_WALLS ARG=rho AT=2.4 KAPPA=10000

# Coordination number
c: COORDINATION GROUPA=bnz GROUPB=prot_noh R_0=0.45

# Metadynamics
METAD ...
ARG=rho,theta,phi
GRID_MIN=0,0.,-pi
GRID_MAX=2.8,pi,pi
SIGMA=0.1,pi/16.,pi/8.
HEIGHT=1.2
PACE=500
BIASFACTOR=20
TEMP=300.
LABEL=metad
CALC_RCT
... METAD


PRINT ARG=rho FILE=distance.dat STRIDE=500
PRINT ARG=metad.* FILE=metad_data.dat STRIDE=500
PRINT ARG=restr.* FILE=sphere_restraint.dat STRIDE=500
PRINT ARG=abs_x,abs_y,abs_z FILE=xyz_coord.dat STRIDE=500
PRINT ARG=rho,theta,phi FILE=rtp_coord.dat STRIDE=500
PRINT ARG=c FILE=all_coordination_45.dat STRIDE=500

FLUSH STRIDE=500