Hi, Well, it's not just a matter of topology. This is only true if the basic assumption holds, that the particles behave approximately classical. This is definitely not the case for species such as hydroxide and hydronium.
Cheers, Tsjerk On Thu, Jul 16, 2009 at 4:13 AM, Justin A. Lemkul<[email protected]> wrote: > > > Marc Charendoff wrote: >> >> Hello, >> >> I am needing to include a single hydroxide ion in my simulation - is >> there a force field available in Gromacs that is already parameterized, or >> do I need to create from scratch? With regards to topology, same question, >> especially as PRODRG does not do mono or diatomics. Any guidance anyone >> could provide would be very much appreciated. I have tried searching the >> archives but didn't find anything. >> > > No, you'll need to do it yourself. The topology should be trivial - two > atoms, one bond. As for what parameters to assign, there you've got your > work cut out for you. > > -Justin > >> Thanks >> Marc Charendoff >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
