[gmx-users] force evaluation

Florian Dommert dommert at fias.uni-frankfurt.de
Tue Jan 6 22:04:02 CET 2009 

* Berk Hess <gmx3 at hotmail.com> [2009-01-06 20:20:40 +0100]:

>
>Hi,
>
>There could be several issues here.
>I don't know how you treat the real space cut-off.
>Could you be seeing charge groups issues?
>You should make sure that each charge group consists of a single atom.
>

Hello,

  since only single positive and negative charges are involved, the
  charge groups consist of single atoms.

  A further point could be the LongRange correction of the Ewald sum, but
  my epsilon_surface=0, so this term should be zero, too.

  Cheers

  Flo


>Berk
>
>> Date: Tue, 6 Jan 2009 18:01:16 +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 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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-- 
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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