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?
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?
Any suggestions will be helpful.
Thanks in advance.
Regards
Sai Ramadugu
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Received on Thu Aug 25 2011 - 09:30:04 PDT
