As I stated in the first sentence, I doubt the usefulness of classical
MD for simulating crystallization of NaCl. Whatever I state after that
applies to the case of trying it with classical MD nonetheless. Please
read closely before trying to outwit however you find on this list.
Second, as is clearly mentioned on the site you gave, the only
relevant interactions in an argon only system are the repulsion and
dispersion. That's what makes it easy. For Na/Cl you have these nasty
electrons, which start to do their thing when Na+ and Cl- get packed
together. That makes it a bit more complicated than argon
condensation/freezing.
Tsjerk
On Sat, Jun 28, 2008 at 5:10 PM, Vitaly Chaban [EMAIL PROTECTED] wrote:
Tsjerk,
Well, the best way would be AIMD, no doubt.
William,
Look here
http://www.mpibpc.mpg.de/groups/grubmueller/start/teaching/vorlesung_computerbiophysik_2004/p4/index.html
for an example how freezing/melting of argon is processed by means of
GROMACS.
TW Hi William,
TW I'm not very sure you can simulate crystallization of salt with
TW classical MD. In any case, the force field is not parameterized to
TW reproduce crystallization or melting c.q. the melted state of NaCl.
TW It's therefore unlikely that it will produce meaningful results. The
TW best approach :) would be to determine parameters for Na/Cl for this
TW purpose.
TW Cheers,
TW Tsjerk
TW On Sat, Jun 28, 2008 at 8:47 AM, Vitaly Chaban [EMAIL PROTECTED] wrote:
I see no problems to use gromacs for it. You make find the parameters
in /top/ions.itp (include ions.itp to your topology) in your gromacs
directory.
Then you can use 'genconf' to create a system of the desired size.
hi gmx users,
Can Gromacs be used to simulate NaCl crystallization and melting?
If it could, where can I find pdb/top/itp etc. input files? Thanks in
advance.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svobody sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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