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 ? Thanks With Regards Gurpreet
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