VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 01 2010 - 07:37:44 CST

hi igal,

On Mon, Feb 1, 2010 at 7:10 AM, Krigel, Igal
<Igal.Krigel_at_safenet-inc.com> wrote:
>    Hi All,
>
>
>    I'm trying to run a LAMMPS output I've made via VMD, and experience some
>    issues with it.
>
>     The output can be downloaded from this link - https://rcpt.yousendit.com/812300172/90846c44ac0c310b22d8ce3607254fcd
>
>    It looks like the format is not read well in VMD and therefore can't be
>   recognize (not the atoms, or the number of frames).
>
>    I will highly appreciate if you can issue some fix to the attached file
>    format (the enclosed file can be viewed in any text editor), or if you
>    point me to the changes I need to do in the format, so I could program it
>    myself, to create a format that is acceptable by VMD.

the main issue is, that you have a varying number of atoms/particles
and VMD expects the number of atoms to be constant. this is a very
fundamental issue and not easy to fix without seriously impacting the
normal scenario of VMD (classical bio simulations, where the number
and identity of atoms and bonds remains constant).

there are a few hacks that one can implement to deal with this
(check out: http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/,
or http://sites.google.com/site/akohlmey/software/topotoos (the varxyz
feature for xyz format trajectories) ), but if you are after convenience and
don't need a VMD-only feature you may be better off using a different
program to visualize your results. a lot of people seem to use atomeye
for those kind of systems, for example.

cheers,
   axel.

>
>
>    Can you please comment on the request and help me?
>
>    Best regards,
>
>    Igal Krigel
>
>    Technical Support Engineer
>    B.Sc Nuclear engineering , M.Sc Nuclear engineering
>    Aladdin Knowledge Systems
>    Support team: +972-3-9781266
>    Direct: +972-3-9781338
>    Fax: +972-3-9781010
>    Mobile: +972-54-6730401
>    Email: igalk_at_aladdin.com
>
>
>
>    From: Krigel, Igal
>   Sent: Sunday, January 31, 2010 10:27 AM
>   To: 'brandon_at_ks.uiuc.edu'
>    Cc: 'yehuda zeiri'; 'Isaac Jacob'
>    Subject: running LAMMPS output via VMD
>
>
>
>    Hi David,
>
>
>
>    I'm hoping that I reached the right person and not causing you any
>    trouble.
>
>
>
>    I'm trying to run a LAMMPS output I've made via VMD, and experience some
>    issues with it.
>
>
>
>    It looks like the format is not read well in VMD and therefore can't be
>   recognize (not the atoms, or the number of frames).
>
>    I will highly appreciate if you can issue some fix to the attached file
>    format (the enclosed file can be viewed in any text editor), or if you
>    point me to the changes I need to do in the format, so I could program it
>    myself, to create a format that is acceptable by VMD.
>
>
>
>    Thank you for your time J
>
>    Best regards,
>
>  Igal Krigel
>    Technical Support Engineer
>   B.Sc Nuclear engineering , M.Sc Nuclear engineering
>    Aladdin Knowledge Systems
>    Support team: +972-3-9781266
>    Direct: +972-3-9781338
>    Fax: +972-3-9781010
>    Mobile: +972-54-6730401
>    Email: igalk_at_aladdin.com
>
>
>
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> --
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>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.