[gmx-developers] New mdp parameter

[Berk Hess]

Florian Dommert wrote:
> On 03.06.2010, at 11:50, David van der Spoel wrote:
>
>   
>> On 6/3/10 11:45 AM, Florian Dommert wrote:
>>     
>>> Hello,
>>>
>>> when talking about the next release I have a small request. So far the
>>> splitting parameter of the Ewald routines can just be supplied
>>> indirectly via the parameter ewald_rtol. However as I have almost
>>> finished the implementation of an error estimate for the SPME it would
>>> be very useful to be able to input the splitting parameter beta
>>> directly. So far I always achieved this by patching ewald_util.c, that
>>> calc_ewaldcoeff returns just the positive value of dtol, if the input of
>>> dtol is negative.
>>> So what do you think bout adding a new parameter to the mdp file like,
>>> ewald_beta or ewald_split, that is just used if larger than zero ?
>>>
>>>       
>> For development now you can use the userreal[1234] and userint[1234]. Once it is finished and we decide this should go into gromacs (which is difficult to judge from your mail now) we can of course add options to the mdp file.
>>
>>     
>
> The code for the error estimate is an enhancement of Carsten's g_tune_pme. We implemented most of the error estimate together and currently I am trying to overcome the last problems which arise from the MPI implementation. However if you use g_tune_pme to tune the accuracy of the electrostatic forces you will have a set of parameters: cutoff in real space, cutoff in reciprocal space, interpolation order and the splitting parameter beta. So after tuning your system you can currently input all parameters in the mdp file apart from beta, which is at the moment calculated from the cutoff in real space and ewald_rtol.
>
> The idea of Berk to include it into grompp is in my opinion not that useful because the program should be capable of using multiple processor otherwise the calculations can last very very long.
>   
But the computational time is mostly due to processing the initial
coordinates for one part
of the error estimate, right?
WE discussed changing that to assuming a uniform distribution, which
would make the estimate
coordinate independent as well as more efficient.

Furthermore, the current way cut-off's are usually treated in Gromacs,
using charge-groups and
a neighborlist fixed for 10 steps, requires a very small ewald_rtol,
independently of the PME
accuracy settings. In the next version (not the version to be released
soon) we might change
to buffered, exact cut-off's which would allow the use of larger
ewald_rtol's set by the PME accuracy.

Berk
> Including it into mdrun would in my opinion require an automatic tuning algorithm, but from experience I know that a human's brain can do this much faster. However in case the algorithm should go into the mdrun routine I would suggest to introduce a new integrator mode like "tune". Then the parallel environment is present and the code has just to be enhanced by a suitable algorithm to find parameters for the requested errors and maximal speed.
>
> Cheers,
>
> Flo
>
>
>
>
>   
>>> Cheers,
>>> Flo
>>> --
>>> Florian Dommert
>>> Dipl.-Phys.
>>>
>>> Institute for Computational Physics
>>>
>>> University Stuttgart
>>>
>>> Pfaffenwaldring 27
>>> 70569 Stuttgart
>>>
>>> Phone: +49(0)711/685-6-3613
>>> Fax: +49-(0)711/685-6-3658
>>>
>>> EMail: dommert at icp.uni-stuttgart.de <mailto:dommert at fias.uni-frankfurt.de>
>>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>>> <http://fias.uni-frankfurt.de/~simbio/Florian_Dommert>
>>>
>>>       
>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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>>     
>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
>
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> Phone: +49(0)711/685-6-3613
> Fax:   +49-(0)711/685-6-3658 
>
> EMail: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
>