[gmx-users] Changing constraints algorithm.

Dawid das addiw7 at googlemail.com
Wed Oct 8 21:50:14 CEST 2014

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
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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