[gmx-developers] Tool to estimate the error for SPME

[Carsten Kutzner]

Hi,

On Aug 27, 2010, at 12:14 PM, Florian Dommert wrote:

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> On 08/27/2010 11:38 AM, hess at sbc.su.se wrote:
>> Hi,
>> 
>> Does this already contain the change (wrt the previous g_tune_pme
>> error estimate) of not using the initial coordinates, but a uniform
>> distribution?
>> 
> 
> Hi,
> 
> not so far. I am thinking about the best way to sample the box
> uniformly without meeting the PME grid nodes. My current thoughts are to
> sample the box in (k+1)(k-1) points in every dimension, where k is the
> number of grid points in the respective direction. However I have to
> test if this is enough or too much.
> 
> I put the current code in gromacs to make it easier to Carsten to access
> it and adapt g_tune_pme if desired. At the beginning we wanted to
> incorporate the tool into g_tune_pme, but as g_pme_error is MPI enabled
> problems arise, when an MPI program starts a further MPI program.
> 
> As soon as possible I will implement this and contact Carsten to discuss
> how and if g_pme_error will be incorporated into g_tune_pme.
A convenient way could be to call g_pme_error from g_tune_pme and
then let g_tune_pme parse the output file of g_pme_error. This way the
error estimate could run in parallel on as many processors the user
has at hand for the tuning run.

Carsten

> 
> 
> /Flo
> 
>> Berk
>> 
>> Hello,
>> 
>> finally I have prepared a tool g_pme_error that allows to estimate the
>> error of SPME and tunes ewald_rtol to minimize the error. It is MPI
>> enabled and contains a claim for citing the corresponding reference
>> where the error estimate is described.
>> 
>> Are you interested to put this into the master branch of gmx ?
>> 
>> /Flo
>> 
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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
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> 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