[gmx-users] Re: Problem calculating RMSD with gromos

Justin Lemkul jalemkul at vt.edu
Tue Jul 2 16:57:17 CEST 2013

On Tue, Jul 2, 2013 at 10:51 AM, Melchor S. <msmqbm at cid.csic.es> wrote:

> Hi Tsjerk,
> I read the sae that you say about the PME and the twin cutoff,  but as I
> have seen that a lot of studies in that people use Gromos with PME and a
> Vander Vaals cutoff so small as mine, I didn't change it, for mantain the
> same settongs than in OPLS simulations.
Force fields are very sensitive to these settings, and the value of rvdw is
particularly significant. With PME, rcoulomb is more flexible, but I
generally do not change rvdw.  Recent studies have indeed shown that PME is
superior to RF for the Gromos96 force fields, or at least 53A6.

> About the structures are very similar, in principle, as I can see in VMD
> and
> so on, but for sure I will try your suggestions.
"Similar" is in the eye of the beholder, and without some numeric
definition (e.g. backbone RMSD between structures), I'd be wary of defining
the results as such. Also realize that force fields are not created equal;
all have caveats, some more pronounced than others. I would not necessarily
assume that two force fields produce equivalent results, and part of the
assessment that one must do (before simulating) is to see who has used what
to study what :)




Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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