[gmx-developers] Shift for MARTINI force field?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 21 11:58:55 CEST 2009
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 GROMOS05
>>>> 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 does.
>> In that sense the manual is erroneous.
>> Also note that the dispersion correction is always correct, since it use
>> 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 the
>> 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 gromacs.
> In that sense the manual should give the function that is used in the code.
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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