How to use gmx trjconv to extract the trajectory only for the protein?

User discussions
1

GROMACS version:5.1.5
GROMACS modification: No
Here post your question : How to generate a trajectory only for the protein after the production run.

Hi all gromacs users,
I have run a 20 micro sec production md run under the martini forcefield and now I want to extract the full trajectory with only protein from the md.xtc file along with centering the protein and then I want to generate a .gro file only with the proteins from the md.xtc file.

So, please someone guide me through the steps to be done.
Thanks and Regards,

Sweta.

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Hello,

you can use gmx trjconv -f md.xtc -o protein-only.xtc -n index.ndx where index.ndx is an index file where the protein is defined as a group. I believe it can also center the protein, you’ll have to check the documentation for exact usage.

From the new trajectory you can dump the final file into .gro format using the -dump flag along with the time of the frame you want, still with trjconv.

Regards,
Petter

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Thanks for your suggestion Petter.

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Note that selection of the protein (a default group) does not require any index file.