[gmx-users] force evaluation
dommert at fias.uni-frankfurt.de
Tue Jan 6 16:33:40 CET 2009
* Berk Hess <gmx3 at hotmail.com> [2009-01-06 15:39:41 +0100]:
>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.
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
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
>> 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 ?
>> > Mark
>> > _______________________________________________
>> > gmx-users mailing list gmx-users at gromacs.org
>> > 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 gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> Florian Dommert
>> 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
>Express yourself instantly with MSN Messenger! Download today it's FREE!
>gmx-users mailing list gmx-users at gromacs.org
>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 gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Computational and Theoretical Softmatter & Biophysics group
Frankfurt Institute for Advanced Studies
60438 Frankfurt am Main
Phone: +49(0)69 / 798 - 47529
Fax: +49(0)69 / 798 - 47611
EMail: dommert at fias.uni-frankfurt.de
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Size: 194 bytes
Desc: not available
More information about the gromacs.org_gmx-users