[gmx-users] Changing constraints algorithm.

[Mark Abraham]

You should start by following all the advice here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark

On Wed, Oct 8, 2014 at 9:50 PM, Dawid das <addiw7 at googlemail.com> wrote:

> 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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