[gmx-users] Stabilizing a heavy metal ion in solution

[Mark Abraham]

On 13/07/2010 3:52 PM, Francisco Garcia wrote:
> Dear users,
>
> I would like to know if users can give me a couple of suggestions on
> how to control large temperature swings of a heavy metal ion like
> Uranium in solution. The temperature of the metal ion fluctuates
> considerably and hardly stabilizes--even in the long time limit while
> the solvent temperature stabilizes easily. The gromacs 'what not to
> do" list strongly discourages against coupling  the ion and solvent to
> separate thermostats. I would like to know if experienced users can
> give tips on how to alleviate this problem.
>    
Probably the variation you are seeing is that expected for a single atom 
- temperature depends on the average KE, of course. The temperature of 
the solvent is being averaged over many more atoms, and unsurprisingly 
has lower fluctuations. You could measure the temperature of a single 
water molecule to see how that compares.

Mark