[gmx-users] Counter ions problem

[Pedro Alexandre Lapido Loureiro]

> Dear GMX users,
> 	I'm new to Gromacs and I have started playing around with the Spider 
> Toxin Peptide tutorial. Everything worked fine, except the chloride ions 
> addition. The genion command replaced two water molecules with Cl to 
> neutralize the toxin +2 charge, but the ions were placed far away from 
> the toxin (on the edge of the box) instead of being placed near some 
> positive charge of the peptide (other programs do it this way, like cion 
> from AMBER). Is this behavior normal or something went wrong with 
> genion? And in that case what is your advice?
> 
> Thanks in advance, Andrea.
> 
> 

Maybe you have used the flag "-random  yes" with genion? 

Cheers,
Pedro.

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil