I refuse to act as a mailing-list subsitute. And there are others better fit to point you to:
http://www.catb.org/~esr/faqs/smart-questions.html http://wiki.gromacs.org/index.php/Parameterization Tsjerk ---------- Forwarded message ---------- From: oguz gurbulak <[email protected]> Date: Sun, Mar 15, 2009 at 2:50 PM Subject: using oplsaa in Gromacs To: [email protected] Dear Dr. Tsjerk, I study on Molecular Dynamics. I'm planning to do md simulations for pure and binary mixtures of n-alkane molecules. I use Gromacs 4.0.4. I want to use oplsaa, but in order to create gro and top files I should create a .itp file manually or enter a new residue for each n-alkane molecule into ffoplsaa.rpt file. I also searched about this to learn much about these procedures. I saw your mails in mail archive and though that you can lead me to do the right thing. I want to ask you which is the true and easy way : 1. To create a .itp file manually residue for each n-alkane molecule 2. To enter a new residue for each n-alkane molecule into ffoplsaa.rpt Could you please give me the information about these procedures ? I would be very grateful if you can help me to choose the right way. Also, Can I use ffG43a2 force field for n-alkane md simulations ? Thank you very much for your attention. Sincerely, Oguz GURBULAK Ege University - Faculty of Science Department of Physics e-mail: [email protected] -- 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://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
