[gmx-developers] Shift for MARTINI force field?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 21 09:01:02 CEST 2009
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.
> gmx-developers mailing list
> gmx-developers at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
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
More information about the gromacs.org_gmx-developers