[gmx-users] Reading multiple trajectories for Gromacs analysis

Ganesh Shahane ganesh7shahane at gmail.com
Wed Feb 10 19:28:56 CET 2016

Hello Anu,

If you have the trajectories like 1-5 ns, 6-10 ns, 11-15 ns, etc, then you
could concatenate all of them in to one single trajectory using the
g_trjcat tool in gromacs an then use g_rms on it to calculate the RMSD.
Hope this helps.

On Wed, Feb 10, 2016 at 6:14 PM, anu chandra <anu80125 at gmail.com> wrote:

> Hello all,
> I just finished a 100 ns simulation using Gromacs, where I ran the
> simulation with a 5 ns window (ie. now I have 20 .trr files with 5 ns data
> in each).  As I am quiet new to Gromacs, I just wonder how can I read all
> the 20 trr files one-by-one to do some basic Gromacs analysis. For e.g if I
> would like to see the change in RMSD along the 100 ns of simulation time,
> how should I read the all trr files to do the calculation with g_rms? I do
> aware that a small shell script will do the job, but I just wonder if there
> is a little more straight way to do it in Gromacs itself.
> Any suggestions would be highly appreciated
> Anu
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Best Regards,
Ganesh Shahane

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