[gmx-users] Counter ions problem
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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