[gmx-developers] Shift for MARTINI force field?
Lars.Schaefer at mpi-bpc.mpg.de
Lars.Schaefer at mpi-bpc.mpg.de
Wed Oct 21 13:11:36 CEST 2009
also check out this (older?) paper of some of the same authors, where they
clarify the issue (in the appendix)
> XAvier Periole wrote:
>> On Oct 21, 2009, at 9:41 AM, Berk Hess wrote:
>>> David van der Spoel wrote:
>>>> Michael Shirts wrote:
>>>>> I noticed this in a paper from van Gundsteren's group:
>>>>> "Since this shift function was erroneously described in the GROMACS
>>>>> manual and also erroneously implemented in the GROMACS program, as
>>>>> has been extensively investigated and reported in ref. 25, we did not
>>>>> want to use exactly the same (inconsistent)
>>>>> shift function, but the shift function as implemented in the
>>>>> biomolecular simulation software."
>>>>> Just checking, this has been addressed now, correct?
>>>> Interesting, for your information I published the correct shift
>>>> function in 2006 (unnoted by Van Gunsteren) in
>>>> http://dx.doi.org/10.1021/ct0502256 (note that this also contains the
>>>> first publication of the OPLS switch function :) along with a whole
>>>> range of other commonly used shift functions). I think (but I'm
>>>> biased) that the equations in that paper are correct, and I'm pretty
>>>> sure the implementation at that time (gmx 3.3) matches the equations,
>>>> but this could easily be checked by running mdrun -debug with shift
>>>> functions, since this will dump the tables, don't have time right now,
>>>> any volunteers? That means that the only thing to fix is the manual.
>>> The code gives (and has always given, as far as I know) continuous
>>> potential, force and second derivative.
>>> The formula in the manual does not describe correctly what the code
>>> In that sense the manual is erroneous.
>>> Also note that the dispersion correction is always correct, since it
>>> the spline table data as input.
>>> But I don't see how the code is erroneous.
>>> There is surely no discontinuity.
>>> I would say that the minimum demands on a shifting function are that
>>> is continuous and differentiable. Since a shifting function is
>>> you are completely free to choose the shape of it as you want.
>> You are right, the only problem is when people try to reproduce results
>> (need to use the same function) a change of the shift function could
>> affect the
>> results. This was observed when comparing MARTINI with gromos and
>> In that sense the manual should give the function that is used in the
> If indeed the code is correct, and has been, maybe we should respond to
> this? The original quote from the article (above) says that both the
> manual and the code are wrong, which is puzzling. Obviously, the manual
> should describe the code accurately. If it does not the manual is wrong.
> But how does one define that a shift function is "wrong" (see e.g.
> appendix of my paper mentioned above)?
> Maybe it is best to fix the manual with a reference to the Van Gunsteren
> paper, and to also state that, in contrast to the paper, the code has
> been correct for a long time.
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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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