AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri May 30 2008 - 12:59:35 CDT

-- On Fri, 5/30/08, Robert Duke <rduke_at_email.unc.edu> wrote:

> From: Robert Duke <rduke_at_email.unc.edu>
> Subject: Re: AMBER: Sander instead of PMEMD
> To: amber_at_scripps.edu
> Date: Friday, May 30, 2008, 8:28 AM
> Err, why can't you use lam, or mpich 1 or 2?

Years ago, I attended a meeting where a famous Japanese chemist, at the end of his talk, was asked why he was always using gold compounds as catalysts for his syntheses of natural products. He answered "I like gold".

May be, on this vein, I can answer "I like open".

francesco

>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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