* Berk Hess <[email protected]> [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
BerkDate: Tue, 6 Jan 2009 18:01:16 +0100 From: [email protected] To: [email protected] Subject: Re: [gmx-users] force evaluation * Berk Hess <[email protected]> [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: [email protected] >> To: [email protected] >> Subject: Re: [gmx-users] force evaluation>> >> * Berk Hess <[email protected]> [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: [email protected] >> >> To: [email protected] >> >> Subject: Re: [gmx-users] force evaluation>> >> >> >> * Mark Abraham <[email protected]> [2009-01-07 00:13:00 +1100]: >> >> >> >> > Suman Chakrabarty wrote:>> >> >> On Tue, Jan 6, 2009 at 2:29 PM, Florian Dommert >> >> >> <[email protected]> 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 >> >> > _______________________________________________ >> >> > gmx-users mailing list [email protected] >> >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> >> > Please search the archive at http://www.gromacs.org/search before posting!>> >> > Please don't post (un)subscribe requests to the list. Use the www interface >> >> > or send it to [email protected].>> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php>> >> >> >> -- >> >> 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: [email protected]>> >> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert >> > >> >_________________________________________________________________ >> >Express yourself instantly with MSN Messenger! Download today it's FREE! >> >http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ >> >_______________________________________________ >> >gmx-users mailing list [email protected] >> >http://www.gromacs.org/mailman/listinfo/gmx-users >> >Please search the archive at http://www.gromacs.org/search before posting!>> >Please don't post (un)subscribe requests to the list. Use the >> >www interface or send it to [email protected].>> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php>> >> -- >> 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: [email protected]>> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert > >_________________________________________________________________ >Express yourself instantly with MSN Messenger! Download today it's FREE! >http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ >_______________________________________________ >gmx-users mailing list [email protected] >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting!>Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [email protected].>Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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: [email protected] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert_________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected].Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 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: [email protected] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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