[gmx-users] Changing constraints algorithm.

[Mario Fernández Pendás]

Dear all,

A question arises to me when thinking about the more robustness of LINCS
with respect to SHAKE: is it well known that LINCS preserves the
symplecticness of the Verlet integrators?

Thank you very much.

Best regards,
Mario

2014-10-08 22:31 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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