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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>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 /><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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