VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 20 2011 - 11:17:34 CDT

On Wed, Apr 20, 2011 at 11:23 AM, Phelan Jr., Frederick R. Dr.
<frederick.phelan_at_nist.gov> wrote:
> The default when you read in a LAMMPS trajectory file to VMD is to display
> the atoms without bonds.
>
>
>
> Is there a tool/script that generates the bond topology from the LAMMPS
> “.data” file associated with the “.lammpstrj” file which can then be
> incorporated using topotools?

yes. and it is already well documented:

http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-readlammpsdata-file-name-atom-style

axel.

>
>
>
> On the topotools page
> (http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---introduction),
> I see that there is information about building a LAMMPS data file from
> molecular data in VMD, so essentially, this is the reverse of that process.
>
>
>
> Thanks,
>
> Fred
>
>
>
>
>
>
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>
>
> ________________________________
>
> Frederick R. Phelan Jr., Ph.D.
> Complex Fluids Group
> Polymers Division
> National Institute of Standards and Technology
>
> ________________________________
>
> NIST, Bldg. 224/Rm. A209
> 100 Bureau Dr., STOP 8542
> Gaithersburg, MD 20899-8542
> 301.975.6761 (VOX)
> 301.975.4924 (FAX)
> Frederick.Phelan_at_nist.gov
>
> My Polymers Home Page
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.