VMD-L Mailing List

From: Ali Osman Acar (aliosmanacar1897_at_gmail.com)
Date: Wed Apr 07 2021 - 15:50:54 CDT

Hi Axel,
The native part doesn't change in time I guess. This is the 1.9.4
documentation and still same after 20 years. :D
https://www.ks.uiuc.edu/Research/vmd/vmd-new/ug/node26.html

As Josh suggested, calling the plugin explicitly will solve the problem I
think.

Vermaas, Josh <vermaasj_at_msu.edu>, 7 Nis 2021 Çar, 23:23 tarihinde şunu
yazdı:

> 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 $dcd_file*
>
> According to the link below, it seems like VMD doesn't natively understand
> lammps traj files. So you can convert your traj file
>
> one of the supported formats given in the link and load them as above.
>
> https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node21.html
> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node21.html__;!!HXCxUKc!lemKqcmnHa2PFM-hKSkdY-WFUsR4c8HF70zDy65RVGjyeOMIuK00f6YuK2Sn8QQ$>
>
>
>
> 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
>
>