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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