[gmx-users] adding ions with genbox

Tyler Luchko tluchko at gpu.srv.ualberta.ca
Tue Mar 2 20:55:01 CET 2004


I am a new user to GROMACS and I would like to add ions to my system.
Rather than adding ions with genion I had hoped to add them with genbox in
random locations without water.  I would then equilibrate the system using
the SD integrator for several nanoseconds.  However, when using genbox to
add my ions all random positions are accepted, even if they are embedded
in my protein and overlap with several atoms.  Checking the archives it
seemed that something similar to this has come up before but I could find
no solutions.  Does anyone have any recommendations?

Thank you,


(_    Tyler Luchko                                  Graduate Student    _)
 _)   Department of Physics                    University of Alberta   (_
(_    Edmonton, Alberta, Canada                                         _)
 _)   780-492-5519                               tluchko at ualberta.ca   (_

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