[gmx-users] Few queries about microsecond long simulations

anu chandra anu80125 at gmail.com
Tue Aug 18 12:42:29 CEST 2015

Dear Gromcas users,

I am planning to do microsecond long simulation of membrane-protein system
and I have ~100,000 atoms in the systems. Since I am trying for microsecond
long simulations and I have a quiet large system, it can generate large
amount of data and in this regard I would like to clarify few queries
before continue the simulations. My queries are,

1. How often I should save the trajectories? In general, I have seen that
mostly use 2ps interval for saving trajectories, as shown below. Will it be
safe if I use 10ps ( 5000 steps ) interval for saving trajectories?

nstxout         = 1000          ; save coordinates every 2 ps
nstvout         = 1000          ; save velocities every 2 ps
nstenergy       = 1000          ; save energies every 2 ps
nstlog          = 1000          ; update log file every 2 ps

2. How safe if I just write only the compressed .xtc file of the
trajectories and not the .trr file during the production run? If its safe,
how can I tell mdrun not to write the trr file?

3. Do I really need the trr file for any MD analysis?

Many thanks in advance


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