[gmx-users] Polarizative models for water

[David van der Spoel]

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.

I would not recommend this model for production though. The model by 
Lamoureux et al. is equally simple but has better properties.

> Sincerely,
> Dmitri
> -----------------------------------------------------------
> On Mon, 28 Apr 2008 10:49:38 +0200
>  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Dmitri Dubov wrote:
>>> (for David van der Spoel, imho)
>>>
>>> Dear David,
>>>
>>> I am doing some similations of large water cluster with tip4p 
>>> flexible model. I would like to include polarizability effect in the 
>>> simulation, but trying it get twofold problem.
>>>
>>> First, I need the input gro-file with dummy and shell particles. I 
>>> failed to apply your utility "mkyaw" to my tip4p-structure file 
>>> directly, since it remained in final file virtual sites MW. Then I 
>>> reduced my tip4 structure to spc and generated correct gro-file with 
>>> dummy and shell and without virtuals MW. But! I see that coordinates 
>>> of both dummy and shell particles coincide with oxygen atoms! Is it 
>>> acceptable or the result of some mistake of mine?
>>>
>>> I cannot examine this (and it is the second problem), since I don't 
>>> understand how topology file should be generated. I find here the 
>>> instruction "to use sw.itp instead of spc.itp". But formal 
>>> replacement in pdb2gmx option "-water" is impossible. Should I
>>> #include "sw.itp"
>>> into top-file manually? Is it enough? Could you give me more detailed 
>>> instructions?
>>>
>>> And the last question. As I know at least three polarizative models 
>>> of water are implemented in GMX. The sw.itp file with your 
>>> parametrization is in GROMACS distributives, the file of parameters 
>>> for Roux group's model can be found in gmx-users archive. What about 
>>> the third model (I mean the model of Gunsteren group)? Is it possible 
>>> to get their parameter file?
>>>
>>
>> You can easily make it yourself. Read chapter 5 in the manual and read 
>> the paper carefully.
>>
>> For mkyaw you should check the extra flags (mkyaw -h).
>>
>> You don't need pdb2gmx anywhere for water clusters.
>>
>>
>>> Thank you in advance
>>>
>>> Sincerely,
>>> Dmitri
>>>
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>>
>>
>> -- 
>> 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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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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