[gmx-users] Simulations in extreme conditions

Justin Lemkul jalemkul at vt.edu
Fri Feb 14 23:09:21 CET 2014

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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