[gmx-users] Different Coulomb energy between gromacs and my calculation
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 21 09:13:36 CEST 2005
On Wed, 2005-07-20 at 15:33 -0700, Tanping Li wrote:
> Dear Gromacs users,
> When I choose cutoff in Coulomb term, in my
> understanding, if one pair is within cutoff, I can get
> the exactly same result as Gromacs. I use formular:
the number 1389 is rounded and in strange units. Angstrom maybe?
> But my test result from one charge group and one Na is
> 6.250759; in gromacs, I set the step as 0, the result
> is -6.252050.
which number is this? what are you computing?
> It does not look like rundoff. This difference can be
> enlarged in my real calculation between a certain
> residue and waters.
> How does gromacs calculate the coulomb interaction in
> cutoff? Does it calculate between individual pairs and
> fianlly get the sum?
> Thank you very much. I tried all ways. It is really
> hard to find the solution.
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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://xray.bmc.uu.se/~spoel
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