[gmx-users] Counter ions problem

Andrea Bernini andrea.bernini at unisi.it
Tue Aug 19 15:22:00 CEST 2003

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.


Andrea Bernini, D. Phil.
Molecular Biology Dept.
University of Siena
Via Fiorentina 1
53100 Siena, Italy

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