Hi Mark, well, equilibration is a tricy thing: Most simple would be the answer "when all observables level off", but one can wait eternally for that. I usually go the folloing way:
a) has the total system energy levelled off / does it not fall anymore but oscillates around a certain value? b) are the interaction energies for the part of my system of interest stable (for you: the protein/protein or protein/solvent terms) not changin anymore / oscillating around a mean value? An other painfull truth: don't expect anything like an equilibration within 100 ps. After 2 ns most of the system creation effects (too high order of solvent, lacking protein solvation etc.) will vanish, but then comes the interesting part where the small but important changes happen. In general: You NEVER can be sure that your system is equillibrated, there might be changes even after 100 ns. A reasonable time scale for simulations would be ca. 10 ns (if you can afford it computationally), and see what you can gain as information out of this trajectory. Hope this helps you - it's not really a cheerful positive answer, but even in silico, nature is a bitch... ;) Steffen > I have a 290+ residue protein and I recently ran a 200 ps simulation > in a water box with electrostatic cutoff at approximately half the > value of the box dimension. Since there is no heating stage in the > dynamics, I am wondering what guidelines there are for knowing when to > evaluate data from the simulation. There are some interesting > features to the RMSD plot I would like to investigate. But I am not > sure I can analyze the last 100 ps of the dynamics or not. Any help > would be greatly appreciated. > > Thanks! > > > Mark > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de _______________________________________________ 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