[gmx-developers] spurious interactions

[David van der Spoel]

On 04/08/15 11:13, David van der Spoel wrote:
> 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.

To follow up, the 1/0 problem can be circumvented in my case using two 
shells, by
setting GMX_NOPREDICT = 1
Nevertheless this should be fixed for the 5.x table routine implementation.

>
>>
>> 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