[gmx-users] Effect of time step size
Justin Lemkul
jalemkul at vt.edu
Thu Feb 12 13:50:00 CET 2015
On 2/12/15 4:58 AM, Faezeh Pousaneh wrote:
> Dear Justin,
>
> Thank you. Yes, both correspond to same setting except dt.
>
> No, expected value is not known.
>
> I have just tried to re-simulate with different values of lincs_itr and
> lincs_order (2 and 8 respectively) and I get similar values for densities.
> Could that be a good solution?
>
In principle, you shouldn't have to do that in situations like these (note the
descriptions of these options in the manual indicate only very specific cases
should require increasing them beyond default). More likely, the agreement
after these changes indicates that there was something unstable about the
previous setup, such that the model is not producing reliable physics when you
increase dt too much.
-Justin
--
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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