[gmx-users] Problem in genion

C.RAMYA ramya at research.iiit.ac.in
Wed Jun 6 15:04:10 CEST 2007


   I am facing a problem while trying to neutralize my molecule.
My molecule is a protein and after writing input file[.tpr] on seeing a
charge of 6.00000e+ i am trying to neutralize it by using 6 CL- ions. when
i have tried 'genion' for small molecules it was running fine,but for this
molecule it has been running since 2 days.
The only message being shown is that only 1 CL- has been introduced.Can
you please help me out with the necessary steps needed.
I am actually new to Gromacs,so please help me get through and if possible
suggest some good material.


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