Hi Justin Should I try to do position restraint at 500k and then full MD simulation. shahid
On 4/27/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > shahid nayeem wrote: > >> My peptide is 26 residue alpha helix obtained from crystal structure .pdb >> file. I am posting energy minimization, position restarint and full MD >> simulation .mdp file >> >> > > <snip> > > >> ref_t = 300 300 >> > > Here, you're equilibrating at 300 K... > > <snip> > > ref_t = 500 500 >> > > and here, you're running MD at 500 K, without any equilibration in between. > That could be a problem, but more likely, the high temperature is simply > causing the structure to break down. Short helices are usually not stable > in isolation, and heating them to extreme conditions will probably > accelerate this process. The various results you're seeing with different > helices may just reflect that you haven't simulated long enough to see > convergence in the structural features, but from what you've described, I > expect what you're seeing is entirely normal, and almost predictable. > > -Justin > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.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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