I guess you have not listed all the dihedrals in the configuration of a ethanol
molecule.
In your .top file, there are only two dihedrals, you might need to include all
others.
By the way, check the other part of your topology to avoid other incorrect
inputs.
Best regards.
Yue Shao
silvester.thu
2008-05-14
发件人： Jussi Lehtola
发送时间： 2008-05-14 11:28:31
收件人： Discussion list for GROMACS users
抄送：
主题： RE: [gmx-users] Energy minimisation problem
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.
--
------------------------------------------------------
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
------------------------------------------------------
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
------------------------------------------------------
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