For my simulations I use ptraj's randomizeions function to achieve what
you are asking for (see page 120 of the AmberTools v1.4 Manual).
-Hugh Heldenbrand
Graduate Student, University of Minnesota
Ajay Ummat wrote:
> I want to add 150mM Na+ Cl- ions in my system. I used the command: addions x
> Na+ 91 Cl- 96 (as my system had +ve 5 charge and I needed 96 each of Na+ and
> Cl-). When I visualize the result of adding ions, leap has added all the
> ions only on one particular side of the protein. This certainly seems
> unreasonable. Can anyone suggest me a way of uniformly distributing the ions
> around the protein. When I say uniformly I mean to consider eletrostatics of
> the distribution. A skewed distribution of charges would make my production
> run unrealistic and unreliable. Thanks in advance.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 30 2010 - 12:00:04 PDT
