AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Fri May 30 2008 - 10:06:42 CDT

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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