[gmx-users] problem with genion

gurpreet singh gps.iitm at gmail.com
Sat Jul 14 10:14:10 CEST 2007

Hello users,

I am carrying a protein simulation using g43a1 force field in gromacs 3.3
 i carried out some intial simulation without water in the absence of the
neutralizing ions
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.
i am using
genion -s 4min.tpr -o 4min_ion.pdb -nname CL- -nn 6 -g 4min_ion2.log

i have checked upto 4min.tpr , structure is fine but only after adding ions
i am getting this breakage i.e in the  file  4min_ion.pdb

what could be the reason for this ?

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 ?

With Regards
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