[gmx-users] problem with genion

[Tsjerk Wassenaar]

Gurpreet,

>  my system was going fine at that time but when i used the genion command to
> add ions , i found that my protein was broken into parts.
>  what could be the reason for this ?

PBC?

>  While running the genion it usually asked for the group into which we want
> to add the ions so i have checked with both the SOL group and OTH group
> seperatly , in both the cases ions were replacing the solvent molecules.  Is
> their any way by which we can add ions without replacing any solvent
> molecules ?

No, there's no space to put them.
Well, you could try to squeeze them in here or there manually, and
perform energy minimization...

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623