Project ID: plumID:20.015
Source: EMMI-ASCT2/3-ANALYSIS/3.1-ASSEMBLE-XTC/plumed_driver.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# include topology info
MOLINFO STRUCTURE=../../0-TOPO/step5_charmm2gmx.pdb

# define all atoms
prot: GROUP NDX_FILE=../../0-TOPO/index.ndx NDX_GROUP=PROT

# make protein whole
WHOLEMOLECULES ...
ADDREFERENCE 
ENTITY0=1-6701         REF0=5.3607,4.5911,3.1497
ENTITY1=6702-6741      REF1=3.2439,3.3684,6.0308
... WHOLEMOLECULES

# PRINT ATOM POSITIONS
DUMPATOMS STRIDE=1 FILE=traj.gro ATOMS=prot