[gmx-users] g_potential: better precision
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 30 08:26:35 CET 2006
이 선주 wrote:
> Dear All,
> I am trying to calculate membrane potential from the charge density. I
> have calculated membrane potential from the charge density profile
> obtained from g_potential function. But I've got unmatched potential
> between block-averaged(10 ns *6) potential and the potential from the
> whole trajectory (60 ns *1). Roundoff error in charge density
> calculation was the reason for the unmatched potential. So I am
> wondering if anyone can guide me so that I can increase the precision of
> the charge density in the output file of g_potential. Any suggesion will
> be appreciated!
You get more averaging in longer stretches of trajectory. As long as
your interface doesn't move both results should be valid.
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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