Re: [AMBER] mmpbsa

From: Jason Swails <>
Date: Fri, 18 Jun 2010 08:59:51 -0400


The entropy will be similar, but not necessarily identical. You will also
not get identical results if you compile nab with and without the intel MKL
using just The only difference between the two programs that I
can see is that different diagonalization algorithms are used, but we've
verified that both algorithms give exactly the same answer (the one chosen
in was chosen because it performed faster in our test set).

A couple things to keep in mind: can run in parallel via a
"forking" method that spawns new compute threads. This is restricted, as
far as I can tell, to shared memory machines. runs in parallel
via MPI, so it can run on distributed memory systems (i.e. it is not
confined to a single node). Only the most recent version of
available has the ability to run in parallel. You can find it at . Do not forget to add
the patches to the script. Also in order to run in parallel, you have to
compile the mpi4py package (instructions on the website).

Good luck!

On Fri, Jun 18, 2010 at 7:30 AM, RANAJIT SHINDE <> wrote:

> Dear Amber members,
> I have done free energy calculations with the script. Now i
> want
> to calculate the entropy with the script as it can be save time
> by
> run in parallel. Will both scripts provide same entropy if parameters are
> kept constant?
> Regards,
> Ranajit Shinde
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jun 18 2010 - 06:00:19 PDT
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