[gmx-users] force evaluation

[Florian Dommert]

* 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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