AMBER Archive (2009)

Subject: RE: [AMBER] pmemd vs sander.MPI

From: Ross Walker (
Date: Wed Nov 04 2009 - 12:33:23 CST

Hi Taufi,

> I am using sander.MPI to run a dynamics simulation with a restraint
> mask
> Molecular Dynamics for 2ns - only Surface atoms are fixed
> can i run the above with pmemd by changing the last two lines
> Molecular Dynamics for 2ns - only Surface atoms are fixed

Yes. PMEMD just needs the old restraint syntax. There is a tool called
ambmask in $AMBERHOME/exe/ which will convert an AMBER mask into the old
group format for you.
> Also, i do remember talking with Dr. Walker about pmemd being faster
> and
> just as accurate as sander.MPI, is that also true when using 32 or 64
> processors, or is it especially true when using large number of
> processors?

It will be a LOT faster. If you are running simulations within PMEMD's
feature set you should probably always use it since it will be faster even
on 1 processor. On 32+ it will make a big difference. You should be seeing
performance equivalent to the following (this was run with pmemd)

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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