[gmx-users] using rerun to extract energies for protein fromtrrfile
Dastmalchi.s at tbzmed.ac.ir
Wed Jan 14 13:01:46 CET 2009
That is what I do. I select just protein group.
From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Wed 2009/01/14 02:20 ب.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] using rerun to extract energies for protein fromtrrfile
Siavoush Dastmalchi wrote:
> Dear Mark,
> Many thanks for your kind suggestion. I did all sorts of things as you suggested, however still I get the same error. Here are the commands that I use (I used grompp also to generate different tpr files):
> $ tpbconv -s fullmd.tpr -n index.ndx -o tpxout.tpr
> $ trjconv -f md_traj.trr -n index.ndx -s tpxout.tpr -o trajout.trr
> $ mdrun_d -s tpxout.tpr -o md_prot_final.trr -c md_prot_final.gro -e md_prot.edr -g md_prot.log -rerun trajout.trr
> I am a bit confused and don't know what I am doing wrong. Is there any way to extract coordinates of just protein molecule for different frames and then calculate their energies (this is just a guess)?
Select just the protein group from the index file when using the *conv
utilities? (I haven't actually ever done this procedure, but that's
about how it should work)
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
A non-text attachment was scrubbed...
Size: 4936 bytes
Desc: not available
More information about the gromacs.org_gmx-users