[gmx-users] Polarizative models for water
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 30 12:12:08 CEST 2008
Dmitri Dubov wrote:
> On Tue, 29 Apr 2008 16:49:24 +0200
> David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Dmitri Dubov wrote:
>>> Dear David,
>>> Thanks for your short but instructive reply. Now I've start the
>>> simulation with your SW-model and see that it runs tenfold slower
>>> than analogues simulation with non-polarizative TIP4P water cluster.
>>> An energy minimization of the shell particle positions is so
>>> time-consuming, isn't it? How can I minimize the energy only at every
>>> Nth step?
>> You can not. However you could give the shell particle a small mass,
>> make it a normal particle and then run normal MD. You would have to
>> recheck the properties though.
> Yes, I see. Should I apply in this case a low temperature (~1 K) to D-S
> relative motion? I do not quite understand how could it be done...
That is possible. It would be good to check density, DHvap and structure
again if you simulate like this. Note that in particular the structure
of the SW model is quite poor.
>> I would not recommend this model for production though. The model by
>> Lamoureux et al. is equally simple but has better properties.
> Unfortunately, SSWM4-DP model has only rigid version, and I need
> flexible one. Maybe I am wrong?
I see. Then I suggest to check the literature a bit more.
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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