[gmx-users] Pressure annealing in Gromacs?

[Jussi Lehtola]

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.)

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