[gmx-users] total charge

[Anton Feenstra]

Lei Zhou wrote:

> Dear gmx-users,
> 
> I am doing a simulation with a small molecule (20 atoms), which
> carries a net charge of -1. To calculate the solvation energy, I need
> to simulate the molecule in water. To get a good estimate
> of the electrostatic interaction between that molecule and water,
> should I do the MD without counter ions added? If I add counter ions
> to neutralize the system, will those ions affect the final result
> (they will interact with the molecule) ? I am using a cutoff of 0.9
> and PME for electrostatic treatment.

In principle your system should be neutral, in practice it may not be 
critical. It would be interesting if you had salt-concentration 
dependent experimental solvation energies, and do the full comparison. ;-)


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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