From owner-chemistry@ccl.net Tue Nov 25 06:16:02 2008 From: "Vincent Leroux vincent.leroux*o*loria.fr" To: CCL Subject: CCL: Ewald Sum Message-Id: <-38171-081125050537-3912-dZAAYqL1AYVv6agw14YamQ ~~ server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Nov 2008 10:24:14 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux,+,loria.fr] Hi Leyla, You really should not try to understand Ewald sum method straight from source code, even if in this case it is well documented. The Ewald sum is done in Fourier space so first make sure you master this mathematical concept. http://en.wikipedia.org/wiki/Fourier_transformation http://en.wikipedia.org/wiki/Ewald_summation Then if you want, try to see how the conversion to Fourier space is handled in the code, how the summation is done, how code is optimized so that terms that can be computed once and for all are grouped in the setup routine, etc. The routine here is particularly simple! Actual MD programs such as NAMD rely on the same principles but with a good number of additional optimizations, in particular the code is heavily parallelized. This is much more complex, hopefully you do not need to master the code in order to understand and perform MD... For theoretical basis of molecular mechanics I strongly recommend you read A.R.Leach's book, if not done already. http://www.booksites.net/leach2/molecular/molecular_modelling_2.html Good luck for your PhD ^^ VL Leyla Ramin lram5228%%usyd.edu.au a écrit : > Sent to CCL by: "Leyla Ramin" [lram5228[A]usyd.edu.au] > I am PhD student in Sydney university and I am working in molecular dynamic simulation, The codes in fortran language in your website in part:sources, allen-tildesley-book "http://www.ccl.net/cca/software/SOURCES/FORTRAN/allen-tildesley-book/index.shtml>" > is so useful for me. > In the "FICHE F.22. ROUTINES TO PERFORM THE EWALD SUM" the routine is > so complicated to understand the method. I am wondering if I can get more information about this code. > Please kindly advise me and thanks for your consideration. > > Best Regards > Leyla Ramin > >