VMD-L Mailing List

From: Ali Osman Acar (aliosmanacar1897_at_gmail.com)
Date: Wed Apr 07 2021 - 14:07:11 CDT

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>, 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
>