Quoting Xavier Periole <[EMAIL PROTECTED]>: > > You do not want to couple the whole system to one bath. Due to the > exchange of kinetic energy between water and protein you'll end up > with a frozen protein and warm water. > > This is simply due to the different behavior of the water and the > protein relative to the integration of the equation of motion. > Integration errors are much more on the solvent, which warms it up; > the use of constraints removes kinetics energy on the direction of > the bonds and proportionally more on the protein, which cools down. > Thus, even if these effects are very small they add up to make the > solvent warmer than the protein cooler. Coupling the whole system > to one bath would thus generate energy exchange to compensate the > temperature difference. On top of this the bath would tend to decrease > the temperature of the whole system although only the solvent is > getting warmer. The protein ends up frozen.
I am going to analyze a few of my simulations to see this effect. I have not done much aqueous MD (and thus perhaps I should hold my tongue instead of giving bad advice!) In my membrane protein MD, my T-coupling groups have been divided (i.e., protein, bilayer, solvent/ions), in line with your suggestion above. In aqueous, however, I have only worked with very small peptides and protein fragments. I was wondering then, doesn't one need to have a large enough group of atoms to get proper statistics? And how small can a group be and still be considered large enough to have its own T-coupling group? Thanks for any insights; your recommendations above are very interesting. -Justin > > I would suggest to Justin to check the temperature of your protein and > your solvent separately. You should see this effect. > > The suggestion of Mark to couple the ion to the part of the system it > belongs to (protein or solvent) is certainly the best. ======================================== 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 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
