[gmx-developers] Shift for MARTINI force field?
x.periole at rug.nl
Wed Oct 21 09:28:02 CEST 2009
On Oct 21, 2009, at 9:01 AM, 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.
I could do, but to clarify your email:
You mean that the code (if incorrect) should have been modified in
versions following gmx3.3 and therefore comparing gmx3.3 to
gmx4.0.X would indicate if it is correct in gmx3.3 since it is correct
in gmx4.0.X ?
Also for your information. The derive of temperature reported by Moritz
et al. (linked by Michael) when using MARTINI with increasing time step
is actually due to (the old story reported by van Gunsteren et al.)
of the average of the half-time-step velocities to get the on-step
temperature instead of the average of the half-time-step kinetic energy.
We have written a comment on that paper ... nothing wrong with
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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> 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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