[gmx-users] Saving trajectories of a particular group within the system

[Junqiao Lee]

Hi All,

I'm conducting a simulation of insulin unfolding in water for a long
period of time (20 ns or more). There were approximately 7800++ SOL
molecules in the system. I'm using tip4p water molecules to solvate my
system.

I intend to generate only the trajectories of my protein alone,
without outputing trajectories of the solvents. This is since the
output files can get really massive. So looking at the manual, I've
inserted the line: "xtc_grps = Proteins" into the .mdp input file and
did a short simulation to try it out.

However, after the run I've examined the .g96, .xtc, .trr, etc.. files
and found that the whole system (Protein + SOL) were outputted,
instead of just the Protein itself.

I've also tried generating my own index file to feed into grompp, but
that didn't help either.

What could be the plausible problem? I'm currently using Gromacs/3.3.3.

Thanks for the advise. Attached below is a cut&paste of my .mdp input
file for the simulation.

-Wade

=================================================
title = Molecular dynamics simulation at 500K
cpp = /usr/bin/cpp
integrator = md
dt = 0.001
nsteps = 1000
nstcomm = 10
comm-mode = Linear

xtc_grps = Protein
nstxout = 50
nstvout = 50
nstfout = 0
nstxtcout = 50
nstlog = 50
nstenergy = 50
nstlist = 10
ns_type = grid

pbc = xyz
coulombtype = pme
rlist = 1.0
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 4.0
compressibility = 4.5e-5
ref_p = 1.0
Tcoupl = Berendsen
tc_grps = System
tau_t = 2.0
ref_t = 450.
gen_vel = no
gen_seed = 94839
constraints = All-bonds
constraint-algorithm = lincs
=================================================