[gmx-users] Changing constraints algorithm.

[Dawid das]

Well, what happens in my system is that water molecule which is actually
near the edge of
solvation box cannot bo settled after ca. 50 ns of simulation. Obviously I
use periodic
boundary conditions. Could you give me any tip about what is wrong if I
provide you
with files you need? If so, what files would you need?

Best wishes,
Dawid Grabarek

PS I read samowhere, that it may be due to fact that this water molecule is
hit
by something and this water did not expect it. But I tried to use brutal
force approach
and to restart the calculations couple of times but each time I run into
the same error,
although for different molecule.

2014-10-08 13:33 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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