[gmx-users] PME, netcharge, implementation, counterions

Alan Wilter Sousa da Silva alan at lac.inpe.br
Fri May 14 16:27:06 CEST 2004

I think the same.  I also heard about calculating heat capacity.  Did you?

I'm going to do it for some simulations here.  Tell more later.

David van der Spoel wrote:

> On Fri, 2004-05-14 at 13:21, Alan Wilter Sousa da Silva wrote:
>>David van der Spoel wrote:
>>>It is quite obvious because one usually only has a few ions. Then it
>>>takes long before they sample the entire volume of the box. You could
>>>say that the ions have reached equilbrium when the ion density in the
>>>whole box is uniform when averaged over the simulation (or in fact the
>>>density of all molecules in the box).
>>And as far as you concern dear Dr. van der Spoel, how long it could be 
>>for a common system of protein in water with a couple of ions (~50000 
>>atoms)?  Less than 100 ps?
> No idea! But it is quite easy to check by running g_density with, say, 1
> nm slabs. Of course the protein should also sample the whole box....
> Another measure would be to check the distribution of ions around the
> protein.

Alan Wilter

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