AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri May 30 2008 - 10:28:24 CDT

Err, why can't you use lam, or mpich 1 or 2? I believe they are all still
available (I just checked the mpich 1 webpage and it is clearly still
available; I still use it on all my own machines, and nothing works
significantly better over ethernet). The original reason I did not support
OpenMPI in amber 9 was the doc was nonexistent. In 10, I flat ran out of
time for adding nice things like support for every compiler and
communications option anyone might find. So sorry if this is a huge
inconvenience, but there are other reasonable options... Typically, you
will have to recompile the mpi implementation to match your fortran compiler
anyway, so it is not a case where the machine shipped with one mpi, and that
is the only one that is going to be convenient to use (I run 3 different
implementations on the 3 machines I use mostly for dev/test - all set up to
be selected by changing a link).
Regards - Bob
----- Original Message -----
From: "Francesco Pietra" <chiendarret_at_yahoo.com>
To: <amber_at_scripps.edu>
Sent: Friday, May 30, 2008 11:17 AM
Subject: Re: AMBER: Sander instead of PMEMD

>
> Hi:
> That added clarity to the matter. Thanks. The point is, however, that we
> users of Amber10/openmpi-1.2.6 - without a special skill with
> compilation - would like to benefit from pmend once we have a firm hint
> how to configure for the compilation. I mean OS Lixux.
>
> francesco pietra
>
>
> --- On Fri, 5/30/08, Florian Haberl
> <Florian.Haberl_at_chemie.uni-erlangen.de> wrote:
>
>> From: Florian Haberl <Florian.Haberl_at_chemie.uni-erlangen.de>
>> Subject: Re: AMBER: Sander instead of PMEMD
>> To: amber_at_scripps.edu
>> Date: Friday, May 30, 2008, 8:06 AM
>> Hi,
>>
>> On Friday, 30. May 2008 16:32, Cristina Sisu wrote:
>> > Thanks Bob,
>> >
>> > Then I think I will give it a try with sander. Fingers
>> crossed!
>> > But are you sure that pmemd does not support mm_pbsa?
>> Because according
>> > to the mmpbsa tutorial, it should work
>> >
>> http://amber.scripps.edu/tutorials/advanced/tutorial3/section2.htm.
>> >
>>
>> the mm pbsa analysis is a post analysis, so you have to
>> seperate the snapshots
>> and than recalculate it with sander. If the simulation is
>> done with sander or
>> pmemd doesn`t matter, the only difference is than pmemd is
>> faster ;)
>>
>> A small hint before starting mm pbsa analysis: It is faster
>> to transfer the
>> trajectory to your wanted snapshot frequency (normally
>> every 25 or 50ps),
>> before starting mm pbsa analysis.
>>
>> greetings,
>>
>> Florian
>>
>>
>> > Cristina
>> >
>> > Robert Duke wrote:
>> > > The primary advantage pmemd offers is purely
>> speed; there are a few
>> > > minor convenience tweaks here and there, but it
>> is mostly supposed to
>> > > do a subset of sander functionality, not the
>> other way around. So
>> > > there should never be a problem moving back to
>> sander from pmemd, as a
>> > > general rule. Also note that pmemd does not
>> support energy
>> > > decomposition through the idecomp switch, and
>> therefore does not
>> > > support mm_pbsa anyway.
>> > > Regards - Bob Duke
>> > >
>> > > ----- Original Message ----- From: "Cristina
>> Sisu" <csds2_at_cam.ac.uk>
>> > > To: <amber_at_scripps.edu>
>> > > Sent: Friday, May 30, 2008 9:47 AM
>> > > Subject: AMBER: Sander instead of PMEMD
>> > >
>> > >> Dear Ambers,
>> > >>
>> > >> I have a problem running PMEMD on our
>> cluster. As far as I understand it
>> > >> does not seem to be a program problem but
>> rather the way that our
>> > >> cluster is build (on module, environments,
>> etc.). I want to do some
>> > >> MMPBSA calculations on a protein-peptide
>> ligand complex. Can I use for
>> > >> the production run, Sander instead of the
>> PMEMD? With the periodic
>> > >> boundary condition parameter switched on, and
>> using the same input (.in)
>> > >> file as for PMEMD?
>> > >> Would the trajectory obtained in this way be
>> suitable for extracting
>> > >> snapshots necessary for mmpbsa ?
>> > >>
>> > >> Thanks,
>> > >> Cristina
>> >
>> >
>> -----------------------------------------------------------------------
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>> --
>> -------------------------------------------------------------------------------
>> Florian Haberl
>> Computer-Chemie-Centrum
>> Universitaet Erlangen/ Nuernberg
>> Naegelsbachstr 25
>> D-91052 Erlangen
>> Telephone: +49(0) − 9131 − 85 26573
>> Mailto: florian.haberl AT chemie.uni-erlangen.de
>> -------------------------------------------------------------------------------
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>
>
>
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