Hi,
I would expect nearly any cell to deform to a very elongated shape,
unless it contains a solid (crystal). In most cases an elongated
shape has the lowest (electrostatic) energy. Therefore anisotropic
coupling is only useful for crystal simulations.
Berk
> Date: Mon, 1 Mar 2010 10:09:08 +0100
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] Constraining periodic cell
>
> On 2010-03-01 09.49, David Chalmers wrote:
> > David,
> >
> > I get a different simulation result if I use isotropic or anisotropic cells.
> > I am not sure yet which is (more) correct, but I would like to be able to
> > run both types to see. I understand that a constrained anisotropic cell is
> > not completely anisotropic, but a fully anistropic one clearly doesn't work.
> >
> > David
>
> You did not say which algorithm you use either, but making the time
> constant longer might help. However, depending on your system, you may
> need substantial surface tension to keep the system neutral if you do
> use anisotropic coupling. We do not completely understand these effects
> yet, see e.g http://bugzilla.gromacs.org/show_bug.cgi?id=165 for
> additional discussions.
> >
> >
> >>> Dear All,
> >>>
> >>> We are running some simulations using an anisotropic periodic cell. We
> >>> are
> >>> getting 'cell runaway' with the cell becoming very long and thin. This
> >>> appears to being driven by the electrostatics of the system. The
> >>> simulation
> >>> then dies because the smallest cell dimension is less than 2*cutoff.
> >>>
> >>> Is there a way that we can apply some constraints to the periodic cell?
> >> Why not use isotropic pressure coupling?
> >>
> >>>
> >>> Regards
> >>>
> >>> David
> >
> > ________________________________________________________________________
> >
> > David Chalmers Lab: 9903 9110
> > Faculty of Pharmacy, Monash University
> > 381 Royal Pde, Parkville, Vic 3053. Australia
> > [email protected]
> > ________________________________________________________________________
> >
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> [email protected] http://folding.bmc.uu.se
> --
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