[gmx-users] Changing constraints algorithm.

[Justin Lemkul]

On 10/8/14 7:24 AM, Dawid das wrote:
> Dear gromacs experts,
>
> Is it allowed to change constraints algorithm (e.g. from LINCS to SHAKE)
> during
> MD simulation? Let's say that simulation crashes because LINCS constraints
> are
> not satisfied. Can I go from LINCS to shake in the middle of simulation and
> restart calculations from the previous point?
>

If LINCS is failing, it's not because you need a different constraint algorithm; 
it's because something physically unrealistic is happening, and the constraints 
are the first thing to fail.  LINCS is more robust than SHAKE, so if you're 
trying to circumvent this problem by moving to SHAKE, I'd say it's likely futile.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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
http://mackerell.umaryland.edu/~jalemkul

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