> Hi, > I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. > For that I require a well minimized structure. I have minimized my > structure > using steepest descent and conjugate gradient. But the structure seems to > have got struct in a local energy minima. How should I proceed to get a > well > minimized structure in order to go for Normal mode Analysis? > Please suggest any protocol.
Check out links from http://wiki.gromacs.org/index.php/normal_mode_analysis. You will probably want double-precision optimization. If you know enough to observe it's in a local minimum, then you should change some aspect of the structure to get it out of the minimum... Mark _______________________________________________ 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
