Dear Nisha, have look to the plumed plugin in gromacs: http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
you can perform US and Metadynamics calculations. Hope it helps and ------------------------------------------------------------ Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 ------------------------------------------------------------ ________________________________________ Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di nishap.pa...@utoronto.ca [nishap.pa...@utoronto.ca] Inviato: venerdì 6 agosto 2010 17.08 A: gmx-users@gromacs.org Oggetto: [gmx-users] Conformational sampling Hello, I would like to do conformational sampling for my simulation of one glycine in its zwitterionic form in water and obtain a PMF curve to see if the system is equilibrated and that all possible torsions are covered for my 100ns run. I am not sure how to approach this issue. Is there a tutorial I can follow? Do I need to do umbrella sampling and use WHAM to extract PMF? I would appreciate some help! Thanks. Nisha P. -- 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 ------------------------------------------------------------- DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permi...@hsr.it - www.5xmille.org -- 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