Quoting shuai lu <[EMAIL PROTECTED]>: > Hello everyone, > > Here i want to caculate the binding free energy between an ligand and its > receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part
Yes, among other things. Read the manual regarding all the free energy options. Simply setting free_energy = yes will not be everything you need to consider. > > or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md > separately? g_lie will give you an estimate of free energy; I don't know how accurate it is relative to a rigorous thermodynamic integration procedure. > > If run a md by set free_energy as "yes", how shoud i get free energy, just > by g_energy alone or with some special parameter? Check the mdrun output options (-dgdl) > For anther method, can the energy calculated by g_lie programme be thought > as binding free energy? Just as some general advice, search for Gromacs free energy tutorials. There is some good information on the wiki site, and there are some excellent tutorials out there, most notably one written by David Mobley. Many users have found this tutorial to be very informative. -Justin > > Thank you! > > -- > Lu Shuai > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
