[gmx-users] Re : Positive and negative ions move in the same direction under a constant electric field?

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 14 04:16:02 CEST 2007

林揚善 wrote:
> Dear Mark and Tom:
>     Thanks for your answer. In order to modify the term of temperature 
> coupling group, I chose “system” in place of “SOL” when using the genion 
> function. So the temperature coupling in .mdp file became:
> tc_grps    =    System
> tau_t      =    0.1
> ref_t      =    300
> I changed the [moleculetype] with the SOL number and add NA+ and CL- in 
> .top file as I did before. Other procedure and setting in the simulation 
> are the same as I used before.
>     There is not protein in my simulation system. I can’t use “protein” 
> and “non-protein” in tc_grps setting.
>     After 600 ps, the Na^+ and Cl^- do not move in the same direction 
> obviously. In fact, they move slowly and slightly. But I can’t observe 
> that the two different ions move in the opposite direction. Is anything 
> inappropriate in my temperature coupling setting?

It looks reasonable as far as T-coupling goes. Can you generate a
back-of-the-envelope estimate for what you'd expect your electric field
to be able to do in this time in vacuo? 600ps just sounds like almost no
time at all to me. Try a small system with few ions that you can
simulate for longer and see what happens?


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