From: Joseph Heil (jpheil_at_ncsu.edu)
Date: Fri Dec 07 2007 - 20:42:24 CST
One reason may be that NAMD ignores most nonbonded parameters. The
appendix D in the NAMD tutorial provides a brief discussion. (pg 103 in
the windows pdf version).
I hope someone can give a more thorough explanation.
Joseph Heil
NC State University
Xu, Jiancong wrote:
> Hi all,
>
> This might be a silly question, but I looked all over the manual and tutorial, still couldn't find the answer. In the PSF file generated by VMD, the number of nonbonded interactions is almost always zero except in alchemical transformation. And I'm wondering why it's that and where the VDW interactions come from in NAMD.
>
> Thanks,
> Jiancong
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Jiancong Xu, Ph.D.
> Center for Molecular Biophysics
> Building 5700 MS6164
> Oak Ridge National Laboratory
> P.O.Box 2008
> Oak Ridge TN 37830, USA.
> Tel: (865) 241-1537
> Email: jia_at_ornl.gov
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
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