[gmx-users] Re: [gmx-revision] Bug in minimization with long range
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 17 19:05:03 CEST 2006
David Mobley wrote:
> This went out to the revision list and I wanted to follow up on it, so
> I figured this is the place to do it.
> On 8/17/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Fixed bug where the long range forces where discarded during energy
>> minization, normal mode analysis and TPI.
> What branch did the fix go into? Is there any chance of getting a
> patch for this for 3.3 posted in a convenient place (i.e. the
It did go into CVS for 3.3 (and 4.0), just updating minimize.c should be
enough. the patch refers to long range due to ewald/PME, not to
twin-range forces. We think the effect will be minor in most cases, I
tested a minimization in water with l-bfgs actually converged faster
with the new patch. For normal modes it might actually even more
important since that's so dependent on the accuracy of the forces.
However, do you do NM in solvent with PBC?
> My main reason for asking is that I'm doing some things (probably
> including normal mode analysis in the near future) where this will
> probably be important, and I'd rather not have to upgrade to 3.3.1 or
> later to have this fixed. I figure it would be less than ideal to have
> to write a paper where I say, "I did all of the calculations except
> the normal mode analysis and ... in GROMACS 3.3, but NMA and ... in
> 3.3.1," and I don't want to have to rerun all of my other calculations
> that will be in the same paper in a later version of GROMACS.
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> gmx-revision mailing list
>> gmx-revision at gromacs.org
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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