[gmx-users] adding ions with genbox
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 2 21:35:01 CET 2004
On Tue, 2 Mar 2004, Tyler Luchko wrote:
>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?
>(_ Tyler Luchko Graduate Student _)
> _) Department of Physics University of Alberta (_
>(_ Edmonton, Alberta, Canada _)
> _) 780-492-5519 tluchko at ualberta.ca (_
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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