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

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 16 03:43:35 CEST 2010

----- 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.


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