AMBER Archive (2008)

Subject: RE: AMBER: Sander instead of PMEMD

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Fri May 30 2008 - 11:24:39 CDT

Thanks a lot,
Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Florian Haberl
Sent: Friday, May 30, 2008 10:31 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Sander instead of PMEMD

Hi,

On Friday, 30. May 2008 17:17, Francesco Pietra wrote:
> 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.

as pointed out some days ago on the mailing list, openmpi is not official supported for amber.

If tried to compile amber10 with openmpi-1.2.6 and with intel compiler and it works fine, the tests are of course all OK.
i can send you the config file, offlist on monday.

greetings,

Florian

>
> 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
> >
> > -----------------------------------------------------------------------
> >
> > > The AMBER Mail Reflector
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> >
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> >
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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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-- 
-------------------------------------------------------------------------------
 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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