[gmx-developers] New mdp parameter

[Carsten Kutzner]

On Jun 3, 2010, at 12:09 PM, 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
Hi Florian,

I think our original idea to use a parallel g_tune_pme for the fast calculation of the error estimate is not
feasible since many queuing systems will not like the fact that a parallel process spawns
other parallel processes. At the moment, g_tune_pme is a serial process calling mpirun 
via system(). This is already a problem to queueing systems like IBM's loadleveler/poe. So
I would rather not like to make things even more complicated here.

If you cannot further optimize the error estimate such that it is fast enough on a single core, then
I would vote for implementing a separate (parallel) tool to do that which then can easily be
called from g_tune_pme.

Carsten


> 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.
> 
> 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
> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne