[gmx-users] Changing constraints algorithm.

[Mark Abraham]

Hi,

Both of LINCS and SHAKE integrate the equations of motion subject to
holonomic constraints (see their papers, or the Gromacs manual). Both
satisfy the constraints only approximately (in the general case), so
otherwise-symplectic integrators using them have qualitatively the same
property of "symplectic, modulo constraint approximation and any deviations
resulting from using floating-point numbers." Whether any particular
constraint settings on a particular system make an observable deviation
from symplectic integration is probably an open question, but the tools to
tune the approximation exist.

Mark


On Tue, Nov 18, 2014 at 4:50 PM, Mario Fernández Pendás <mariofp77 at gmail.com
> wrote:

> 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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