[gmx-users] how small rcoulomb can be

Mark Abraham mark.abraham at anu.edu.au
Thu Jun 17 00:11:17 CEST 2010

----- Original Message -----
From: Gaurav Goel <gauravgoeluta at gmail.com>
Date: Thursday, June 17, 2010 5:21
Subject: [gmx-users] how small rcoulomb can be
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> For my NPT/NVT simulations I'm using a BKS potential for dispersion
> interactions (VdWtype=USER)  which has a cut-off of 0.55 
> nm. I also
> set rcoulomb=rlist=0.55 nm.
> My first question is regarding the choice of rcoulomb=0.55nm. Any
> thoughts on whether this rcoulomb is large enough to ascertain that
> real space electrostatics interactions are fairly small (in comparison
> to total coulombic interactions)?

That's around half the size of typical rcoulomb values used for PME, so you'll need to adjust ewald_rtol and fourier_spacing to a considerable degree in order that the electrostatics your PME model is comparably accurate. If this model has been used with PME in the past, then you will have some guidance in its literature (though GROMACS does not make it easy to choose beta directly). This will mean the reciprocal-space processors are doing lots more work than normal, and you'll want to set -npme to be half of -np, or maybe zero. Even so, your parallel scaling will be noticeably worse than normal PME.

> My second question is in regards to doing long (~15-100 ns) NVE
> simulations. It appears using coulombtype=PME-Switch will be the best
> option to accurately conserve energy. Any thoughts on how to choose
> rcoulomb_switch and rcoulomb?
> Thanks,
> Gaurav
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100617/3960ed9c/attachment.html>

More information about the gromacs.org_gmx-users mailing list