[gmx-users] reaction field kappa and ionic strength
David van der Spoel
spoel at xray.bmc.uu.se
Fri Mar 23 20:56:48 CET 2007
Daniela S. Mueller wrote:
> dear all,
> there are errors in the code regarding 1) the equation for kappa, which
> is used for the reaction field method; and 2) in the calculation of the
> ionic strength.
> 1) in rf_util.c kappa is calculated as
> *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
> but the factor 2 in the square root is only correct if the sum in the
> ionic strength I is actually divided by 2, which it isn't. so the factor
> 2 should be omitted.
> 2) in force.c the ionic strength is (among others) calculated by summing
> the absolute values instead of the squares of the charges.
> zsq += fabs(q);
> this is only correct for monovalent charge groups.
> @developers: these errors have been remarked previously on the mailing
> list. as it is not mentioned in the bugzilla, i thought i can bring it
> up again... can you correct this in the code for the next version please?
> best regards,
I vaguely recall something like that, probably before bugzilla even. But
could you please submit a bugzilla? Otherwise we might well forget it
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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