Thanks a lot to both of you. Chitrita.
On Wed, Mar 11, 2009 at 2:09 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Chitrita Dutta Roy wrote: > >> Hi Tsjerk, >> >> Did you mean to send you the md.mdp file that I used to run grompp for md >> simulation? I am using Gromacs 4.0.2 versision. I am not very clear about >> the parameters used in mdp files. So I am sending the mdp file here. >> >> > Some consultation with the manual will provide you with the information to > learn about these parameters. They should not be set blindly! > > > cpp = /usr/bin/cpp > > This is an example of one of the obsolete parameters no longer used in > Gromacs 4.0.x, hence grompp told you it would be ignored. > > Tcoupl = V-rescale >> tau_t = 0.1 0.1 >> tc_grps = Protein SOL >> ref_t = 300 300 >> > > Here is the problem, as grompp pointed out to you. You are controlling the > temperature of both the Protein and solvent water (SOL). But your system > contains NA+, doesn't it? So it is not part of any temperature coupling > group. Try "Protein Non-Protein" for simple aqueous systems with ions. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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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