[gmx-users] Pressure annealing in Gromacs?

Jussi Lehtola jussi.lehtola at helsinki.fi
Thu Dec 3 08:22:46 CET 2009

On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: 
> Jussi Lehtola wrote:
> > 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.

Yup, that came to mind but then one ends up with N trajectories and log
files. And one has to run a big pile of grompp commands, that waste some
parallel run time, so I really would like something integrated.

Besides, a thing like changing the reference pressure should be a
no-brainer in the source code - assuming the code is well structured and
one knows it well beforehand.

Anyway, the problem was solved for now already. Still, pressure
annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla
about it.)

Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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