On Thu, Aug 25, 2011 at 12:23 PM, Sai Kumar Ramadugu <sramadugu.gmail.com>wrote:
> Dear Amber Users,
> I am running Jarzynski/SMD simulations for the binding free energy of a
> disaccharide-Protein complex.
> I have started using SANDER module of AMBER with Jarzynksi by setting jar =
> 1 in the md input file.
> Since PMEMD gives more speed in comparison to SANDER, I started using PMEMD
> for pulling simulations.
> I checked the test directory and found that Jarzynksi method passed with
> SANDER but I could not find the Jarzynksi with PMEMD in the test directory
> of AMBER on our cluster.
> To confirm that SANDER and PMEMD give same results I used the same md input
> file for both and saw that the values of work obtained from both the md
> engines are same for first 100-200 steps. But later they diverge.
>
> My questions: Can one use PMEMD and Jarzynski?
>
I believe you can, yes.
> Since I could not find the PMEMD/Jarzynksi in the test
> directory, are we compiling AMBER wrong? Should we check again on the
> compilation of AMBER?
>
No. It means that whoever added Jarzynski pulling to pmemd didn't put in a
test case. I'll look into this. If you compared it to sander and got the
same results (after a couple hundred steps), you should be fine.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 25 2011 - 17:00:02 PDT
