AMBER Archive (2009)

Subject: RE: [AMBER] PDMED

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 09 2009 - 00:19:36 CDT

Hi Catein,

> I am trying to do the PDMED for the dynamics simulations. After
> standard amber10 installation, I found pmemd and pmemd.amba directories
> with src subdirectory for each of them.

Note, it is 'PMEMD'. If you do not plan to run Amoeba calculations, or do
not know what Amoeba is then you do not need to worry about pmemd.amba.

$AMBERHOME/src/pmemd you may wish to build if you plan to run a lot of
parallel jobs and/or large MD runs. PMEMD will be faster than Sander even at
relatively low cpu counts. This has to be built separately from sander.
Essentially:

cd $AMBERHOME/src/pmemd/
./configure

This will bring up a list of options for architectures etc. Take your pick
and away you go...
 
> Do I still need to install the PDMED according to the README file too?

If you want to take advantage of its high speed and scaling yes.

> I would like to do the 10 ns simulation for a protein-DNA-Drug complex
> with explicit solvent TIP3 solvent box. Is it compatible with PDMED?

Yes. PMEMD supports explicit solvent MD (including extra points for TIP4PEW
etc) as well as implicit solvent GB simulations. It does not support
multisander implementations, such as replica exchange, TI etc and it also
does not support QMMM. See the PMEMD section of the AMBER manual for a full
discussion.

Other than that PMEMD will read standard sander input and will write sander
output.

> What can we do next to run the calculations? What is the step need to
> be done so as to use PDMED in supercomputer system?

Do you have a supercomputer? Or access to one? If so then you need to build
(or buy someone a pint so they build it for you) PMEMD on said supercomputer
linking to the correct MPI libraries etc for the machines interconnect. You
can then run PMEMD on said supercomputer using scripts appropriate for the
queuing system in use. For some up to date benchmarks see:
http://ambermd.org/amber10.bench1.html

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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