[gmx-users] Protocol for Gromacs analysis

anu chandra anu80125 at gmail.com
Wed Mar 2 17:33:16 CET 2016

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

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


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