RE: vmd-l: Gromacs analysis tools for Namd output

From: Kei Sit (kei.sit_at_qut.edu.au)
Date: Wed Feb 01 2012 - 17:33:01 CST

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Hi Paul,

I have personally used GROMACS to analyse NAMD output files. I use a bit of a workaround for this.

First I use catDCD and convert the .dcd file to a .trr file. This format is readable in GROMACS. I did find however that GROMACS reads the time slightly differently (I kept getting 400ps instead of 4ns). I emailed the GMX email list and the reply was to use trjconv and specify the timestep of 1 (or whatever it is for you). I don't seem to be losing any information here so I'm quite confident it works fine. Also, if you've been using VMD to create your .psf and .pdb files, you'll soon run into the problem that the Histidine residues (if you're doing protein stuff) are named differently. I have had to rename all Histidine residues to HIS instead of HSE HSP and HSD.

Hope that helps!

Cheers,
Jacky

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of PAUL NEWMAN
Sent: Thursday, 2 February 2012 3:42 AM
To: namd-l_at_ks.uiuc.edu; vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Gromacs analysis tools for Namd output

Dear NAMD and VMD users,

I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition I installed VMD 1.9 and set up VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is located the dcdplugin.so )

I verified that VMD_PLUGIN_PATH is pointing out to the right folder. However when I run for example

g_rmsf_d -f file.dcd -s file.pdb

I got the following error

The file format of file.dcd is not a known trajectory format to GROMACS. Please make sure that the file is a trajectory!

GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.
This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.

No plugin for dcd found

Am I doing something wrong? Do I need to do something else?

Any help and advise will be highly appreciate it

Thanks so much for the help

--
Cheers,
Paul

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