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

David van der Spoel spoel at xray.bmc.uu.se
Mon May 14 07:33:33 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?

your system is probably not equilirated before 600 ps. genion doesn't
use the temperature coupling information, just mdrun.
please compute the msd (g_msd) and see when the curve becomes a straight
line. you'll have to run at least 5 ns.

> Can anyone give me some clue on this? I’ll appreciate for any hints on 
> this question.
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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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