I meant pmend. I have always compiled sanderr with ifort/openmpi, including amber10 and openmpi-1.2.6. Perhaps there is only a problem with mkl/parallel for qmmm, perhaps restricted to certain hardware, see the thread. My problem is to compile pmend on openmpi
Thanks
francesco
--- On Fri, 5/30/08, Florian Haberl <Florian.Haberl.chemie.uni-erlangen.de> wrote:
> From: Florian Haberl <Florian.Haberl.chemie.uni-erlangen.de>
> Subject: Re: AMBER: Sander instead of PMEMD
> To: amber.scripps.edu
> Date: Friday, May 30, 2008, 8:31 AM
> 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.chemie.uni-erlangen.de>
> wrote:
> > > From: Florian Haberl
> <Florian.Haberl.chemie.uni-erlangen.de>
> > > Subject: Re: AMBER: Sander instead of PMEMD
> > > To: amber.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.cam.ac.uk>
> > >
> > > > > To: <amber.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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> --
> -------------------------------------------------------------------------------
> 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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Received on Sun Jun 01 2008 - 06:08:01 PDT
