[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:
> http://dx.doi.org/0.1039/b818713d.
> "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.

> Best,
> Michael
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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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