[gmx-users] Effect of time step size

[Justin Lemkul]

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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