Hello Justin, Thanks for the reply . I apologise for the repeat mail. The parameters are for ffG43a3 forcefield. Yes I am using the default electrotatics cutoff values as an initial run. I would change to PME method as you say. However I was wondering If r_epsilon value equals to 66 contributes to a change in the simulation or this value holds good only if reaction field is on ? sharada -- Original Message -- From: "Justin A. Lemkul" <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Date: Sat, 31 Jan 2009 00:42:36 -0500 Subject: Re: [gmx-users] Melittin in methanol... sharada wrote: > rlist = 0.5 > rcoulomb = 1.4 > rvdw = 0.8 You are using cut-off electrostatics by default, so you are probably getting some bad artifacts (use PME instead). Also, the values of rlist, rcoulomb, and rvdw you are using do not correspond to those for which the Gromos96 force field was derived. These make no sense. Refer to the original literature for whichever parameter set you decided to use. -Justin -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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