AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri May 30 2008 - 09:13:20 CDT

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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