[gmx-users] RE: can gmx be used to simulation NaCl

[Tsjerk Wassenaar]

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 <vvchaban at gmail.com> 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 <vvchaban at gmail.com> 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: chaban at univer.kharkov.ua
> 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