Quoting sudheer babu <[EMAIL PROTECTED]>: > Thank you very much Mr.Andreas for reply, > As I told you, used deprecated FF for protein, after insertion into POPC > bilayer, ran 4ns production. is it compulsory to use opls/gromos43a6 *ff for > run simulation protein in water? I have repeat to the whole process because > wrong usage of depracated *FF. Pls help me.... > Thanks for your invaluable help........ >
I believe it is most advisable to avoid the ffgmx force field. There was a recent discussion on this topic as a matter of fact, so have a look through the list archive from the past few weeks. There is also a paper out from Tieleman's group (2006? 2007?) that recommends using OPLS in conjunction with the Berger lipid parameters to get the best results. You would then have to conduct your simulations in water under OPLS as well to get results that can be compared. -Justin ======================================== 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 [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
