VMD-L Mailing List

From: Kenneth Smith (ksmith_at_ecs.umass.edu)
Date: Tue Jul 13 2004 - 08:27:07 CDT

Hello.
    I am currently working on simulations where we allow the bonding structure to be altered after each time step in the MD simulation. I would like to use VMD as the visualization program, but so far I can not identify any possible trajectory file formats that allow for updated connectivity at every time step. The dynamic bonding method is not sufficient as we may break specific bonds and also at times form bonds with radical molecules which would have the possibility of one additional bond beyond the traditional valance limits. Are there any ways to address these issues with VMD as it is currently written or would this require source code modification?
    Thanks for you help! Ken

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Kenneth D. Smith

Department of Chemical Engineering
University of Massachusetts- Amherst
159 Goessmann Lab
686 N. Pleasant St.
Amherst, MA 01003
Office: 216 Goessmann
tel: (413) 545-2234
fax: (413) 545-1647
email: ksmith_at_ecs.umass.edu