AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri May 30 2008 - 10:17:15 CDT

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
> >
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in
> the *body* of the email)
> > to majordomo_at_scripps.edu
>
> --
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the
> *body* of the email)
> to majordomo_at_scripps.edu

      
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu