I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is actually implemented in FORTRAN.
Jonathan ____________________________ Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 300E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ran Friedman Sent: Wednesday, July 18, 2007 10:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Implicit solvent simulation Dear Tom, The paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: > Hi, > > Just to let people know in case they are unaware there is a paper > where implicit solvent models have been implemented in GROMACS, the > paper can be found using the following link: > > http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid =15814616 > > > Tom > > --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel > <[EMAIL PROTECTED]> wrote: > >> SeungPyo Hong wrote: >>> Thank you for your kind reply, Stephane. >>> Anyhow it is a little disappointing that Generalized-Born is not >>> implemented in Gromacs. >>> >> >> I've put it on the development TODO list (feel free to volunteer) >> >> http://wiki.gromacs.org/index.php/Implicit_Solvent >> >> The reason it is not there is because none of the developers has >> considered it worthwhile. >> >> -- >> David van der Spoel, Ph.D. >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: >> +4618511755. >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se >> _______________________________________________ >> 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 > > > > ---------------------- > TJ Piggot > [EMAIL PROTECTED] > University of Bristol, UK. > > _______________________________________________ > 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 > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ 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 _______________________________________________ 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
