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 <mariof...@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.abra...@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 < > > mariof...@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.abra...@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 <add...@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 <jalem...@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. 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