VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 29 2012 - 14:44:28 CDT

Hi,
  You can use the "DynamicBonds" representation to avoid this difficulty,
in combination with a VDW representation.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 29, 2012 at 03:31:58PM -0400, Phelan Jr, Frederick R. Dr. wrote:
> I am using the following procedure to draw LAMMPS output with bonds in
> VMD:
>
>
>
> 1) Read in the LAMMPS data file: topo readlammpsdata <LAMMPS Data File
> ".data"> full|molecular|bond
>
> 2) Write bond topology to psf file: animate write psf <file.psf>
>
> 3) Delete all existing molecules in memory
>
> 4) Read in the LAMMPS trajectory file < LAMMPS Trajectory File
> ".lammpstrj">
>
> 5) Read in the psf file: animate read psf <file.psf>
>
>
>
> Works great for unwrapped trajectories. However, is there any
> procedure/trick to stop the display of bonds for bonded atoms on opposite
> sides of a periodic boundary without unwrapping?
>
>
>
> Thanks,
>
> Fred
>
>
>
>
>
>
>
> --------------------------------------------------------------------------
>
> 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
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
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