Project ID: plumID:21.018
Source: input/MacroD2_Y190N_input/metad_35ang.dat
Originally used with PLUMED version: 2.6
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

WHOLEMOLECULES ENTITY0=1-3670 ENTITY1=3671-3727

# Group definition
prot_noh: GROUP NDX_FILE=ref_index.ndx NDX_GROUP=Protein-H
ref: GROUP NDX_FILE=ref_index.ndx NDX_GROUP=Prot_ref_noH
AR6: GROUP NDX_FILE=ref_index.ndx NDX_GROUP=AR6_noH 

ref_center: COM ATOMS=ref
AR6_center: COM ATOMS=AR6

Fix: FIXEDATOM AT=5.0,5.0,5.0
Dis: DISTANCE ATOMS=ref_center,Fix

ref_coord: POSITION ATOM=ref_center NOPBC
AR6_coord: POSITION ATOM=AR6_center NOPBC

abs_x: MATHEVAL ARG=AR6_coord.x,ref_coord.x FUNC=x-y PERIODIC=NO
abs_y: MATHEVAL ARG=AR6_coord.y,ref_coord.y FUNC=x-y PERIODIC=NO
abs_z: MATHEVAL ARG=AR6_coord.z,ref_coord.z FUNC=x-y PERIODIC=NO

rel_x: MATHEVAL ARG=abs_z FUNC=x PERIODIC=NO
rel_y: MATHEVAL ARG=abs_x,abs_y FUNC=(sqrt(3)*y+x)/2 PERIODIC=NO
rel_z: MATHEVAL ARG=abs_x,abs_y FUNC=(y-sqrt(3)*x)/2 PERIODIC=NO

rho: MATHEVAL ARG=abs_x,abs_y,abs_z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
siga: MATHEVAL ARG=rel_z,rho FUNC=sqrt(-x+y) PERIODIC=NO
theta: MATHEVAL ARG=rel_x,rel_y FUNC=atan2(y,x) PERIODIC=-pi,pi

rmsd: RMSD REFERENCE=ref_protein_noH_nosite.pdb TYPE=SIMPLE

# Restraining potential of the sphere
restr_dis: UPPER_WALLS ARG=Dis AT=1.00 KAPPA=20000 OFFSET=0
restr_rho: UPPER_WALLS ARG=rho AT=3.50 KAPPA=20000 OFFSET=0
restr_siga: UPPER_WALLS ARG=siga AT=1.0 KAPPA=20000 OFFSET=0
restr_rmsd: UPPER_WALLS ARG=rmsd AT=0.10 KAPPA=20000 OFFSET=0

# Coordination number
c: COORDINATION GROUPA=AR6 GROUPB=prot_noh R_0=0.45

# Metadynamics
METAD ...
ARG=rho,siga,theta
GRID_MIN=0,0,-pi
GRID_MAX=3.6,1.2,pi
SIGMA=0.1,0.04,pi/8
HEIGHT=1.2
PACE=500
BIASFACTOR=20
TEMP=298
LABEL=metad
CALC_RCT
... METAD

PRINT ARG=metad.* FILE=metad_data.dat STRIDE=5000
PRINT ARG=restr_dis.*,restr_rho.*,restr_siga.*,restr_rmsd.* FILE=sphere_restraint.dat STRIDE=5000
PRINT ARG=ref_coord.x,ref_coord.y,ref_coord.z FILE=ref_coord.dat STRIDE=5000
PRINT ARG=AR6_coord.x,AR6_coord.y,AR6_coord.z FILE=AR6_coord.dat STRIDE=5000
PRINT ARG=rho,siga,theta FILE=rtp_coord.dat STRIDE=5000
PRINT ARG=c FILE=all_coordination_45.dat STRIDE=5000
PRINT ARG=rmsd FILE=rmsd.dat STRIDE=5000
PRINT ARG=Dis FILE=distance.dat STRIDE=5000

FLUSH STRIDE=5000