[gmx-users] Energy minimisation problem

[Kukol, Andreas]

You should also do some MD and then look at your molecule and trajectory (bond lengths, angles, etc.), if it becomes distorted. If that is the case, there might be something wrong with your topology.

If everything is fine, you should use the energy minimised molecule to build the box, EM again and then MD.

Not sure about the energies. Maybe they should be negative ?

Andreas

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Jussi Lehtola
> Sent: 14 May 2008 04:28
> To: Discussion list for GROMACS users
> Subject: 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
> jussi.lehtola at helsinki.fi, p. 191 50673
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
>
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