[gmx-users] Protocol for Gromacs analysis

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 2 18:00:11 CET 2016

Hi Anu,

If your protein is a multimer, removing PBC should be removing jumps (-pbc
nojump). Otherwise you may get problems with RMSD and radius of gyration
and such. You should then assert that the reference structure is also in
one piece.

For the rest your approach looks fine. And, no, steps 1 and 2 cannot be

Hope it helps,


On Wed, Mar 2, 2016 at 5:33 PM, anu chandra <anu80125 at gmail.com> wrote:

> Dear Gromcas users,
> I am quite new to Gromacs and I have just completed 100 ns simulation of a
> membrane protein using Gromcas. Now, I would like to do some basic analysis
> like RMSD, RMSF, Hydrogen bonding etc with the 100 ns trajectories. Below,
> I just wrote down the steps I adapted to generate the necessary preparatory
> files for different analysis with Gromacs analysis tools. I will be
> grateful if the experts in the community can help me with the their
> suggestion, if I am doing anything wrong here.
> Step-1 : Concatenate all the trajectories, which I have run as 5 ns window
> each, and generate a single 100 ns trajectory.
> gmx trjcat -f 1md.trr 2md.trr 3md.trr 4md.trr 5md.trr 6md.trr 7md.trr
> 8md.trr 9md.trr 10md.trr -o 1_10md_concat.xtc
> Step-2: Remove the PBC
> gmx trjconv -f 1_10md_concat.xtc -o noPBC.xtc -s md.tpr -pbc mol -ur
> compact
> Step-3: Make the necessary index file if one want to do analysis with any
> specific group of atoms/molecule
> gmx make_ndx -f md.gro -o index.ndx
> Step-4: Do the analysis with different Gromcas analysis tools ( gmx rmsd,
> gmx cluster etc.) using the files from step-2 and step-3
> Am I doing any thing wrong here? Is there any fine tuning required in these
> steps? Is there a way to combine the steps 1 and 2?
> Many thanks in advance
> Anu
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Tsjerk A. Wassenaar, Ph.D.

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