On 2012-11-11 17:26, Justin Lemkul wrote:
On 11/11/12 11:22 AM, Ali Alizadeh wrote:
Dear Justin
Thank you for reply,
I want to simulation of water freezing, my condition:
pressure=300 bar and T=240 k , number 1656, run time= 100ns,
I can not see regular structure of ice by MD simulation or by gromacs?
In your opinion, if i want this structure of ice for my simulation,
What can i do?
Start by searching the literature for a suitable protocol. Ice
simulations have been done before. As I said before, each water model
has a different melting point, and hardly any of them correspond to the
actual experimental value. See if you can produce a suitable simulation
with a pressure of 1 bar (proof of concept) and then change conditions.
What you have to keep in mind is that most water models were designed to
work at ambient conditions for "normal" simulations. They do not
necessarily work under extremes or produce useful results under those
conditions.
-Justin
Try TIP4P/Ice
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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