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Hi,<br><br>There could be several issues here.<br>I don't know how you treat the real space cut-off.<br>Could you be seeing charge groups issues?<br>You should make sure that each charge group consists of a single atom.<br><br>Berk<br><br>> Date: Tue, 6 Jan 2009 18:01:16 +0100<br>> From: dommert@fias.uni-frankfurt.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] force evaluation<br>> <br>> * Berk Hess <gmx3@hotmail.com> [2009-01-06 17:00:06 +0100]:<br>> <br>> ><br>> >Hi,<br>> ><br>> >I don't understand what the exact difference is you are referring to.<br>> >In Gromacs the direct space part for Ewald and PME uses identical<br>> >code with identical input.<br>> <br>> Hello,<br>> <br>> sorry I forgot to mention that we have a tool that calculates the<br>> electrostatic interaction with the Ewald method and the SPME algorithm.<br>> From this program I get a reference force that can be tuned to a<br>> certain precision, since Kolaffa and Perram have already<br>> investigated the error introduced by the Ewald summation. This yields<br>> as a reference force. Here arises the first problem:<br>> If I use the same parameters and the Ewald summation the forces in<br>> gromacs and our tool differ in about 10^-4. That should not be since<br>> the forces should be exact up to 10^-12.<br>> A further problem comes up when comparing forces derived with a very<br>> small splitting parameter beta. This means the error stems from the<br>> direct part. However the error estimate of Kolaffa and Perram fails for<br>> the forces calculated by gromacs. The force deviation calculated with our tool<br>> fits to the estimate, so our code seems to be correct.<br>> <br>> Cheers,<br>> Flo<br>> <br>> >So or both Ewald and PME are right or both are wrong.<br>> ><br>> >Berk<br>> ><br>> >> Date: Tue, 6 Jan 2009 16:33:40 +0100<br>> >> From: dommert@fias.uni-frankfurt.de<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: Re: [gmx-users] force evaluation<br>> >> <br>> >> * Berk Hess <gmx3@hotmail.com> [2009-01-06 15:39:41 +0100]:<br>> >> <br>> >> ><br>> >> >Hi,<br>> >> ><br>> >> >The error should not be in the tables, if you are using Gromacs 4.<br>> >> >We made sure that the accuracy of the tabulation and interpolation<br>> >> >is nearly the full precision (both in single and double precision).<br>> >> ><br>> >> >For these kind of testing purposes you should be using double precision<br>> >> >anyhow, which gives you far more accuracy than 10^-4.<br>> >> <br>> >> Hello,<br>> >> <br>> >> of course Gromacs 4 compiled with double precision is used and I even<br>> >> get a better agreement with my reference force, if the coulomb forces<br>> >> are tabulated. <br>> >> <br>> >> However where could the difference arise ? <br>> >> <br>> >> I also tried a version without the software implementation of the invsqrt but it <br>> >> doesnt change. If our results would not conincide with the error<br>> >> estimate of Perram and Kolafa, I would say we have a bug in our code.<br>> >> However the estimate is perfect and that for all cases:<br>> >> * Ewald Sum (implemented in Gromacs)<br>> >> * sPME with analytical differentiation (implemented in Gromacs)<br>> >> * sPME with ik-differentiation<br>> >> <br>> >> Cheers,<br>> >> <br>> >> Flo<br>> >> <br>> >> ><br>> >> >Berk<br>> >> ><br>> >> >> Date: Tue, 6 Jan 2009 14:24:17 +0100<br>> >> >> From: dommert@fias.uni-frankfurt.de<br>> >> >> To: gmx-users@gromacs.org<br>> >> >> Subject: Re: [gmx-users] force evaluation<br>> >> >> <br>> >> >> * Mark Abraham <Mark.Abraham@anu.edu.au> [2009-01-07 00:13:00 +1100]:<br>> >> >> <br>> >> >> > Suman Chakrabarty wrote:<br>> >> >> >> On Tue, Jan 6, 2009 at 2:29 PM, Florian Dommert<br>> >> >> >> <dommert@fias.uni-frankfurt.de> wrote:<br>> >> >> >>> Finally it would be very interested in a possiblity to switch off the<br>> >> >> >>> vdw interactions easily. So far I used an appropiate topology files with <br>> >> >> >>> C6<br>> >> >> >>> and<br>> >> >> >>> C12 set to zero. Is there an easier solution as using a table filled<br>> >> >> >>> with zeros ?<br>> >> >> ><br>> >> >> > Zeroed tables will be considerably slower than zeroed parameters.<br>> >> >> ><br>> >> >> > Depending on the way the force field is organized, you might create a <br>> >> >> > version of the force field files that zeroes out these parameters. Another <br>> >> >> > possibility might be to using the preprocessor mechanism to define the VDW <br>> >> >> > parameters only under some circumstances.<br>> >> >> <br>> >> >> Thank you very much for the help. It seems I went the a good way with<br>> >> >> using a preprocessing command to define the zero VDW IA.<br>> >> >> <br>> >> >> Now I have to find where the difference in the calculation of the<br>> >> >> electrostatic forces. Perhaps somebody can tell me, where the forces get<br>> >> >> tabulated, that I can take a look at the code there ?<br>> >> >> <br>> >> >> Cheers,<br>> >> >> <br>> >> >> Flo<br>> >> >> <br>> >> >> <br>> >> >> ><br>> >> >> > Mark<br>> >> >> > _______________________________________________<br>> >> >> > gmx-users mailing list gmx-users@gromacs.org<br>> >> >> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> >> > Please search the archive at http://www.gromacs.org/search before posting!<br>> >> >> > Please don't post (un)subscribe requests to the list. Use the www interface <br>> >> >> > or send it to gmx-users-request@gromacs.org.<br>> >> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >> >> <br>> >> >> -- <br>> >> >> Florian Dommert<br>> >> >> Dipl.-Phys.<br>> >> >> <br>> >> >> Computational and Theoretical Softmatter & Biophysics group<br>> >> >> <br>> >> >> Frankfurt Institute for Advanced Studies<br>> >> >> Johann-Wolfgang-Goethe University<br>> >> >> <br>> >> >> Ruth-Moufang-Str. 1<br>> >> >> 60438 Frankfurt am Main<br>> >> >> <br>> >> >> Phone: +49(0)69 / 798 - 47529<br>> >> >> Fax: +49(0)69 / 798 - 47611<br>> >> >> <br>> >> >> EMail: dommert@fias.uni-frankfurt.de<br>> >> >> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert<br>> >> ><br>> >> >_________________________________________________________________<br>> >> >Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> >> >http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> >> >_______________________________________________<br>> >> >gmx-users mailing list gmx-users@gromacs.org<br>> >> >http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> >Please search the archive at http://www.gromacs.org/search before posting!<br>> >> >Please don't post (un)subscribe requests to the list. Use the <br>> >> >www interface or send it to gmx-users-request@gromacs.org.<br>> >> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >> <br>> >> -- <br>> >> Florian Dommert<br>> >> Dipl.-Phys.<br>> >> <br>> >> Computational and Theoretical Softmatter & Biophysics group<br>> >> <br>> >> Frankfurt Institute for Advanced Studies<br>> >> Johann-Wolfgang-Goethe University<br>> >> <br>> >> Ruth-Moufang-Str. 1<br>> >> 60438 Frankfurt am Main<br>> >> <br>> >> Phone: +49(0)69 / 798 - 47529<br>> >> Fax: +49(0)69 / 798 - 47611<br>> >> <br>> >> EMail: dommert@fias.uni-frankfurt.de<br>> >> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert<br>> ><br>> >_________________________________________________________________<br>> >Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> >http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> >_______________________________________________<br>> >gmx-users mailing list gmx-users@gromacs.org<br>> >http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >Please search the archive at http://www.gromacs.org/search before posting!<br>> >Please don't post (un)subscribe requests to the list. Use the <br>> >www interface or send it to gmx-users-request@gromacs.org.<br>> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> Florian Dommert<br>> Dipl.-Phys.<br>> <br>> Computational and Theoretical Softmatter & Biophysics group<br>> <br>> Frankfurt Institute for Advanced Studies<br>> Johann-Wolfgang-Goethe University<br>> <br>> Ruth-Moufang-Str. 1<br>> 60438 Frankfurt am Main<br>> <br>> Phone: +49(0)69 / 798 - 47529<br>> Fax: +49(0)69 / 798 - 47611<br>> <br>> EMail: dommert@fias.uni-frankfurt.de<br>> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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