VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 07 2021 - 14:59:25 CDT

On Wed, Apr 7, 2021 at 3:22 PM Ali Osman Acar <aliosmanacar1897_at_gmail.com>
wrote:

> 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
>

that link is about a VMD version from 20 (twenty!) years ago.
current VMD does load lammps dump files just fine with the extension
.lammpstrj just fine.

axel.

>
>
> 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
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uL8s_tdUwMRTx_TFM4F44O2rzLT6UJhcN3y-5g36DDbroUEyQRiylkUC2Ga31mFIrQ$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.