On Thu, Sep 20, 2012 at 12:45 PM, Ali M. Naserian-Nik <naseriannik.gmail.com
> wrote:
> Dear Amber users/developers,
>
>
> I apologize, as it is a duplicate message. The following issue is very
> important for me.
>
> I ‘m trying to do some steered MD simulations with pmemd 12 in which the
> distance between two atoms must be increased while the angle made between
> three atoms must be fixed at its initial value. I know that this kind of
> simulations is performable easily by using jar and ncsu_pmd in sander.
> However, it seems that ncsu code is not accessible in pmemd. On the other
> hand, if two restraints are added in the restraint file for steered MD (one
> for increasing the distance and another for keeping the angle constant),
> only the first restraint in the restraint file would be applied and the
> other would be ignored by the code. Is there a way to perform this kind of
> simulations through pmemd 12? I'd be so grateful if anyone could help me on
> these issues.
>
I do not think it's possible with pmemd to perform jarzynski pulling while
restraining another distance. We recently tried doing it and it didn't
appear to work (and with my knowledge of the code, I don't think it's
possible).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 20 2012 - 10:30:04 PDT
