[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?

genion -random

>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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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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