On 2/14/14, 1:58 PM, CipPruteanu wrote:
Hi everyone! I am trying to run a simulation of methane-water mixtures under extreme conditions, that is around 25 kbars and 600K (and maybe higher in both pressure and temperature). I am currently using OPLS for methane with TIP3P for water. The way I proceed is as follows: -generate a box of methane and water having my desired concentration -do an energy minimization for 100ps -do a NVT equilibration at my desired temperature for 100ps -do a NPT equilibration at my desired pressure and temperature for 100ps -run the simulation (NPT) for as long as I desire (1-10 ns for the moment) The simulations I ran on the individual components get reasonably good results for them under these conditions. However, once I put them together, the mixture doesn't behave as expected (by recent experimental findings). Is this approach ok or is there something fundamentally flawed about it ? I know the fact that the forcefields are not meant to be used at these high pressures/temperatures, but apart from that, is there anything I could improve?
I'm assuming that NPT and the data collection period are effectively the same, since you likely don't have anything worth restraining to distinguish any sort of distinct equilibration period. The main question is: do your systems equilibrate at the desired conditions? 25 kbar is a bit crazy for the biomolecular force fields in Gromacs, and given the inherent fluctuations in pressure coupling, I would be a bit surprised if you actually achieved such pressures in that amount of time.
The biggest culprit, in my mind, is the force field. OPLS and other biomolecular force fields weren't designed for extreme conditions like this, and interactions with water under ambient, biological conditions, will be wildly different from what you're trying to do. That's not to say it can't be done, of course, but the "standard" parameters may no longer apply.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
