[gmx-users] Wrtiing pair interaction energy on the fly

sapna sarupria sapna.sarupria at gmail.com
Thu Sep 16 03:52:33 CEST 2010

Thank you Mark for your response. I only need to double check a few things
for which using generic C kernels should suffice. I need to run only 1 or 2
steps and not in parallel.
Thanks again for your help.

On Wed, Sep 15, 2010 at 9:43 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: sapna sarupria <sapna.sarupria at gmail.com>
> Date: Thursday, September 16, 2010 1:35
> Subject: [gmx-users] Wrtiing pair interaction energy on the fly
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Dear all
> >
> > I understand that pair interactions in gromacs are calculated through
> assembly loops. Can some one guide me to the resources using which I can
> write out the interaction energy/force for each pair directly from gromacs
> during the simulation (without using the rerun option). The rerun option is
> especially difficult when you want pair interaction between all atoms of
> one's system since one has to define that many index groups. I most cases
> rerun is good, but in my case I have to test interaction between several
> pairs.
> You are limited to 256 energy groups with or without using -rerun. If you
> need more, then perhaps you should consider some other simulation software
> that is better suited to this task. With GROMACS, you could use an
> environment variable to force the use of the generic C kernels, and inside
> that kernel use printf to write out the energy for each interaction. This
> will be horribly slow, and will be vastly simpler if not attempted in
> parallel.
> Mark
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Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540

Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
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