[gmx-developers] spurious interactions

[David van der Spoel]

On 03/08/15 16:43, Mark Abraham wrote:
> Hi,
>
> 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.

>
> Mark
>
> 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:
>
>     Hi,
>
>     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?
>
>     Cheers,
>     --
>     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>
>     http://folding.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