[gmx-users] Pressure annealing in Gromacs?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Dec 2 16:45:46 CET 2009

Sounds like a phase change. If that is the case, 10 ns is likely not  
enough to expect equilibration considering that bilayers can take 50ns  
(or even substantially longer) to equilibrate the area per lipid after  
a phase change.

None of this is to contradict your intuition about a  
high-temperature/high-pressure pulse.

Jussi Lehtola wrote:
> Hi,
> I'm experiencing trouble converging the density of some heavy liquid
> alcohols (after 10 ns of simulation the density is still changing
> linearly). Is there any way to run pressure annealing in Gromacs?
> Running the system through a high pressure and temperature might give an
> equilibrium structure quicker.

There's nothing native that I'm aware of, but it should be
straightforward to use sed or perl in a script to do the annealing "by
hand" in a series of mdrun invocations.


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