* 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 forcesare 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
BerkDate: 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
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