Project ID: plumID:19.033
Source: pmd_plumednest/plumed.0.dat
Originally used with PLUMED version: 2.3
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

LOAD FILE=PathCV.cpp
UNITS LENGTH=A TIME=ps ENERGY=kcal/mol

#original omega torsion angles 
ow1: TORSION ATOMS=17,19,21,31
ow2: TORSION ATOMS=31,33,35,45
ow3: TORSION ATOMS=45,47,49,59

#shift
cw: CONSTANT VALUE=pi

#shifted omega torsion angles
w1: COMBINE ARG=ow1,cw COEFFICIENTS=1.0,0.5 PERIODIC=-pi,pi
w2: COMBINE ARG=ow2,cw COEFFICIENTS=1.0,0.5 PERIODIC=-pi,pi
w3: COMBINE ARG=ow3,cw COEFFICIENTS=1.0,0.5 PERIODIC=-pi,pi

#non-periodic shifted omega torsion angles (for restraining)
r1: COMBINE ARG=w1 COEFFICIENTS=1.0 PERIODIC=NO
r2: COMBINE ARG=w2 COEFFICIENTS=1.0 PERIODIC=NO
r3: COMBINE ARG=w3 COEFFICIENTS=1.0 PERIODIC=NO

#cosines of original omega torsion angles 
c1: TORSION ATOMS=17,19,21,31 COSINE
c2: TORSION ATOMS=31,33,35,45 COSINE
c3: TORSION ATOMS=45,47,49,59 COSINE

#sum of cosines of original omega torsion angles
W: COMBINE ARG=c1,c2,c3 PERIODIC=NO

#path-CV in the space of w1,w2,w3
#WALKERS_ID=${ID} must be changed for each walker, as well as the name of the plumed.${ID}.dat file
pcv: PATHCV ARG=w1,w2,w3 GENPATH=20,60,20,1.57,1.57,1.57,-1.57,-1.57,-1.57 FIXED=21,80 HALFLIFE=2000 PACE=500 STRIDE=500 WALKERS_RSTRIDE=500 WALKERS_ID=0 WALKERS_N=8 WALKERS_DIR=.

#metadynamics on path progress parameter pcv.s
metad: METAD ARG=pcv.s SIGMA=0.05 HEIGHT=0.02 PACE=500 INTERVAL=-0.1,1.1 GRID_MIN=-1.0 GRID_MAX=2.0 WALKERS_MPI FILE=HILLS

#tube potential to restrain all walkers near the path
tube: RESTRAINT ARG=pcv.z AT=0.0 KAPPA=50.0

#walls to keep walkers near the relevant interval pcv.s=[0,1]
lwall: LOWER_WALLS ARG=pcv.s AT=-0.1 KAPPA=1000.0 EXP=2 EPS=1 OFFSET=0
uwall: UPPER_WALLS ARG=pcv.s AT=1.1  KAPPA=1000.0 EXP=2 EPS=1 OFFSET=0

#walls to avoid periodic crossings in the space of w1,w2,w3
lwwall: LOWER_WALLS ARG=r1,r2,r3 AT=-3.0,-3.0,-3.0 KAPPA=1000.0,1000.0,1000.0 EXP=2,2,2 EPS=1,1,1 OFFSET=0,0,0
uwwall: UPPER_WALLS ARG=r1,r2,r3 AT=3.0,3.0,3.0 KAPPA=1000.0,1000.0,1000.0 EXP=2,2,2 EPS=1,1,1 OFFSET=0,0,0

PRINT ARG=*  STRIDE=50 FILE=COLVAR