[gmx-users] genion

Ran Friedman ran at hemi.tau.ac.il
Thu Jan 6 15:42:18 CET 2005


Alberto Malvezzi wrote:

> Dear Collegues,
> I know his subjec has been discussed alredy, but I still havent got 
> the answer.
> My system has a charge of -12.
> If a use genion with no -random flag, all Na ions are placed on the 
> box wall.
> If I place the -random flag genion works fine, that is, randomly 
> places the Na ions around the protein.
> But I was hoping to to place the ions based on the electrostatic 
> potential, not randomly! 

At least in my experience, when you run the simulation the ions will 
quickly move away from their initial positions anyway, so it makes sense 
to use the -random flag.


> What am I doing wrong?
> Thanks
> Alberto

Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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