[gmx-users] Energy minimisation problem

[Jussi Lehtola]

On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
> On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
> > First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it looks reasonable.
> > 
> Thanks, using the vacuum method I seem to get better results.

It seems I spoke too soon. Energy minimising the one-particle structure
in vacuum gives me the following potential energies:

methanol	21.4
ethanol		9.4
propanol	3.8
butanol		4.1
pentanol	12.2
hexanol		81.0

All minimizations have converged with Fmax < 1e-3. Are these energies
reasonable? The energies of methanol and hexanol are somewhat high.

Energy minimisation with a system of 4913 methanol molecules with
initial density of 500 kg/m^3 and periodic boundary conditions gives as
potential energy Epot = -1.67e5, however the forces do not converge. 
Running the system with Berendsen pressure and temperature thermostats
(p = 1 bar, T = 300 K) results in a crash after 82 ps. The total energy
is positive and of the order 1e5.
-- 
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Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50673
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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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