VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Wed Apr 07 2021 - 15:23:52 CDT

Hi Ali,

I don’t think its that, because Karteek gets it to load through the graphical loading pipeline. VMD 1.9.4 has a lammpstrj molfile plugin, but I think the issues is that it isn’t being called for whatever reason from the addfile path. Karteek, what happens if you explicitly call out the lammpstrj plugin?

molfile addfile dump.lammpstrj type lammpstrj waitfor all

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ali Osman Acar <aliosmanacar1897_at_gmail.com>
Date: Wednesday, April 7, 2021 at 3:44 PM
To: "Karteek K. Bejagam" <karthik3327_at_gmail.com>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Loading files

Hi Karteek,

I'm using NAMD and this is how I load a traj file (DCD) with its structure file in scripts.
mol load psf $psf_file dcd $dcd_file
According to the link below, it seems like VMD doesn't natively understand lammps traj files. So you can convert your traj file
one of the supported formats given in the link and load them as above.
https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node21.html$>

Best,
Ali


Karteek K. Bejagam <karthik3327_at_gmail.com<mailto:karthik3327_at_gmail.com>>, 7 Nis 2021 Çar, 21:11 tarihinde şunu yazdı:
Hello VMD users,

I am trying to write a tcl script for post-processing of LAMMPS MD trajectory.
How can we read residue names from psf file and coordinates from a dump file.

When I load them using VMD polymer.psf dump.lammpstrj, seems to be working fine and I can execute the commands in TK console.

However, when I load them using text mode in a separate file, it does not seem to work properly. These are the commands I am using

mol new polymer.psf waitfor all
mol addfile dump.lammpstrj waitfor all

Did anyone had such an issue and how can we fix this?

Thanks,
Karteek