From: Aron Broom (broomsday_at_gmail.com)
Date: Wed May 30 2012 - 23:14:21 CDT
during classical MD it shouldn't be possible for covalent bonds to break,
so this suggests something is wrong with your forcefield parameters. And
what do you mean by "break"? How large does the distance become? Which
forcefield are you using?
On Thu, May 31, 2012 at 12:09 AM, Kapil jain <noxtreme007_at_gmail.com> wrote:
> Hi all,
> I am running md simulation on homology model of a membrane protein,
> following the membrane protein tutorial. During the minimization and
> equilibriation with protein constrained, the disulfide bond breaks. What
> can be the possible cause for this or does it happens naturally during the
> minimization? Are there any means to preserve disulfide bond?
> Kapil Jain
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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