[gmx-users] force evaluation

Florian Dommert dommert at fias.uni-frankfurt.de
Tue Jan 6 18:01:16 CET 2009 

* Berk Hess <gmx3 at hotmail.com> [2009-01-06 17:00:06 +0100]:

>
>Hi,
>
>I don't understand what the exact difference is you are referring to.
>In Gromacs the direct space part for Ewald and PME uses identical
>code with identical input.

Hello,

  sorry I forgot to mention that we have a tool that calculates the
  electrostatic interaction with the Ewald method and the SPME algorithm.
  From this program I get a reference force that can be tuned to a
  certain precision, since Kolaffa and Perram have already
  investigated the error introduced by the Ewald summation. This yields
  as a reference force. Here arises the first problem:
   If I use the same parameters and the Ewald summation the forces in
   gromacs and our tool differ in about 10^-4. That should not be since
   the forces should be exact up to 10^-12.
  A further problem comes up when comparing forces derived with a very
  small splitting parameter beta. This means the error stems from the
  direct part. However the error estimate of Kolaffa and Perram fails for
  the forces calculated by gromacs. The force deviation calculated with our tool
  fits to the estimate, so our code seems to be correct.

Cheers,
Flo

>So or both Ewald and PME are right or both are wrong.
>
>Berk
>
>> Date: Tue, 6 Jan 2009 16:33:40 +0100
>> From: dommert at fias.uni-frankfurt.de
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] force evaluation
>> 
>> * Berk Hess <gmx3 at hotmail.com> [2009-01-06 15:39:41 +0100]:
>> 
>> >
>> >Hi,
>> >
>> >The error should not be in the tables, if you are using Gromacs 4.
>> >We made sure that the accuracy of the tabulation and interpolation
>> >is nearly the full precision (both in single and double precision).
>> >
>> >For these kind of testing purposes you should be using double precision
>> >anyhow, which gives you far more accuracy than 10^-4.
>> 
>> Hello,
>> 
>>   of course Gromacs 4 compiled with double precision is used and I even
>>   get a better agreement with my reference force, if the coulomb forces
>>   are tabulated. 
>>   
>>   However where could the difference arise ? 
>>   
>>   I also tried a version without the software implementation of the invsqrt but  it 
>>   doesnt change. If our results would not conincide with the error
>>   estimate of Perram and Kolafa, I would say we have a bug in our code.
>>   However the estimate is perfect and that for all cases:
>>    * Ewald Sum (implemented in Gromacs)
>>    * sPME with analytical differentiation (implemented in Gromacs)
>>    * sPME with ik-differentiation
>> 
>> Cheers,
>> 
>> Flo
>> 
>> >
>> >Berk
>> >
>> >> Date: Tue, 6 Jan 2009 14:24:17 +0100
>> >> From: dommert at fias.uni-frankfurt.de
>> >> To: gmx-users at gromacs.org
>> >> Subject: Re: [gmx-users] force evaluation
>> >> 
>> >> * Mark Abraham <Mark.Abraham at anu.edu.au> [2009-01-07 00:13:00 +1100]:
>> >> 
>> >> > Suman Chakrabarty wrote:
>> >> >> On Tue, Jan 6, 2009 at 2:29 PM, Florian Dommert
>> >> >> <dommert at fias.uni-frankfurt.de> wrote:
>> >> >>>  Finally it would be very interested in a possiblity to switch off the
>> >> >>>  vdw interactions easily. So far I used an appropiate topology files with 
>> >> >>> C6
>> >> >>> and
>> >> >>>  C12 set to zero. Is there an easier solution as using a table filled
>> >> >>>  with zeros ?
>> >> >
>> >> > Zeroed tables will be considerably slower than zeroed parameters.
>> >> >
>> >> > Depending on the way the force field is organized, you might create a 
>> >> > version of the force field files that zeroes out these parameters. Another 
>> >> > possibility might be to using the preprocessor mechanism to define the VDW 
>> >> > parameters only under some circumstances.
>> >> 
>> >> Thank you very much for the help. It seems I went the a good way with
>> >> using a preprocessing command to define the zero VDW IA.
>> >> 
>> >> Now I have to find where the difference in the calculation of the
>> >> electrostatic forces. Perhaps somebody can tell me, where the forces get
>> >> tabulated, that I can take a look at the code there ?
>> >> 
>> >> Cheers,
>> >> 
>> >> Flo
>> >> 
>> >> 
>> >> >
>> >> > Mark
>> >> > _______________________________________________
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>> >> 
>> >> -- 
>> >> Florian Dommert
>> >> Dipl.-Phys.
>> >> 
>> >> Computational and Theoretical Softmatter & Biophysics group
>> >> 
>> >> Frankfurt Institute for Advanced Studies
>> >> Johann-Wolfgang-Goethe University
>> >> 
>> >> Ruth-Moufang-Str. 1
>> >> 60438 Frankfurt am Main
>> >> 
>> >> Phone: +49(0)69 / 798 - 47529
>> >> Fax:   +49(0)69 / 798 - 47611
>> >> 
>> >> EMail: dommert at fias.uni-frankfurt.de
>> >> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
>> >
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>> 
>> -- 
>> Florian Dommert
>> Dipl.-Phys.
>> 
>> Computational and Theoretical Softmatter & Biophysics group
>> 
>> Frankfurt Institute for Advanced Studies
>> Johann-Wolfgang-Goethe University
>> 
>> Ruth-Moufang-Str. 1
>> 60438 Frankfurt am Main
>> 
>> Phone: +49(0)69 / 798 - 47529
>> Fax:   +49(0)69 / 798 - 47611
>> 
>> EMail: dommert at fias.uni-frankfurt.de
>> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
>
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-- 
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47529
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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