Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB
Rohit Malshe wrote: Dear all, I want to use a system in which Epsilon AA = 1 and Epsilon BB = 0.5. But I want to use Epsilon AB = 1.5. How do I do that in gromacs? http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB
If you will use Lennard-Jones potential, you can combine both epsilons: AB = sqrt(AA*BB) Osmair Date: Tue, 24 Aug 2010 15:48:56 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB Rohit Malshe wrote: Dear all, I want to use a system in which Epsilon AA = 1 and Epsilon BB = 0.5. But I want to use Epsilon AB = 1.5. How do I do that in gromacs? http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB
On 8/24/10 8:38 PM, Rohit Malshe wrote: Dear all, I want to use a system in which Epsilon AA = 1 and Epsilon BB = 0.5. But I want to use Epsilon AB = 1.5. How do I do that in gromacs? You can specify nonbonded parameters per atompair. Check topology section in the manual. [ nonbond_params] ; i j type c6 c12 O O 1 1 1 N N 1 0.5 0.5 O N 1 1.5 1.5 whatever -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB
The link takes me to the Tab Potentials page, but using the latest Firefox with Mac OS 10.5.8 there are gaps in the text but no functions shown at the top of the page. E.g. generic form is: several blank lines, LJ form is: even more blank lines, etc. On Aug 24, 2010, at 3:48 PM, Justin A. Lemkul wrote: Rohit Malshe wrote: Dear all, I want to use a system in which Epsilon AA = 1 and Epsilon BB = 0.5. But I want to use Epsilon AB = 1.5. How do I do that in gromacs? http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
