[gmx-users] Changing constraints algorithm.

Wed Nov 19 16:02:12 CET 2014

Hi Mark,

Thank you very much for your answer.

Best regards,
Mario

2014-11-19 14:59 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> That work treats the constraint algorithm as a black box that accurately
> computes the Lagrangian multipliers; the abstract is worded as "SHAKE-type
> constraints" etc. So the properties of any other method that computes the
> multipliers satisfactorily (e.g. LINCS) follow immediately.
>
> Mark
>
> On Tue, Nov 18, 2014 at 6:02 PM, Mario Fernández Pendás <
> mariofp77 at gmail.com
> > wrote:
>
> > Hi,
> >
> > Thank you for your answer Mark.
> > I have read the papers cited in the Gromacs manual. However my question
> was
> > more about theoretical results/derivations as the ones explained in the
> > following reference for SHAKE/RATTLE:
> >
> >
> >
> https://stat.duke.edu/~scs/Courses/Stat376/Papers/Constraints/LeimkuhlerSymplecticConstraints94.pdf
> >
> > I would like to know if similar results have been obtained for LINCS.
> >
> > Thank you very much.
> >
> > Best regards,
> > Mario
> >
> > 2014-11-18 17:53 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >
> > > 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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