Ok. You meant I have to cross check these parameters before getting in to simulation.I will do that
Thank you very much for your replies. Dept. Biotechnology Ext. 3108 ----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Wednesday, June 17, 2009 6:35:01 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Marc F. Lensink wrote: > On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: >> The .mdp file seems reasonable. QM charges are not necessarily the end >> result in Gromos parameterization. In fact, such calculations are often >> unnecessary. In my experience, assigning charges based on functional groups >> already present in the force field is often a reasonable starting point. >> But in any case, you must always verify your results and, in the end, >> follow the same parameterization scheme as the original force field (which, >> in the case of the Gromos force fields, does not include QM charge >> calculations). > > I've run hundreds of QM charge calculations. in many cases, they are > remarkably similar to the gromos charges... > Agreed. The point I was trying to make (perhaps poorly) was that simply running a QM charge calculation and calling it done is not the right track. I got the impression from the original post that charges were assigned and a simulation conducted without any validation of those parameters. -Justin > cheers, > marc > _______________________________________________ > gmx-users mailing list gmx-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 > -- ======================================== 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 gmx-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 list gmx-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
