[gmx-developers] spurious interactions
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 4 11:13:39 CEST 2015
On 03/08/15 16:43, Mark Abraham wrote:
> It's hard to say, since AFAIK this code has no maintainer and probably
> only complex/sw as a test. It manages its own call to do_force, so the
> only thing I can suggest is stepping through with a debugger and a
> watchpoint on that nrnb entry for VDW.
It seems that the table routines still use the invsqrt mechanism to
compute a distance. Obviously this breaks when the distance is zero.
This means that with tables we can not use invsqrt - this is a problem
in any tabulated interaction (e.g. softcore for free energy).
Unfortunately this is only part of the problem, since this does not yet
explain how this energy ends up being a Van der Waals interaction.
> On Mon, Aug 3, 2015 at 4:26 PM David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> I just uploaded a new redmine http://redmine.gromacs.org/issues/1791
> about a weird topology where a Van der Waals interaction is computed
> despite all VDW parameters being zero. The interaction is computed
> despite not being in a known neighborlist. Any suggestions where to
> start debugging?
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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