[gmx-users] genbox molecule insertion

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 7 11:18:29 CET 2005

On Mon, 2005-03-07 at 07:38 +0100, Lubos Vrbka wrote:
> hi all,
> from what i've found on the list (and by looking in genbox source as
> well), it seems to me that genbox is currently broken in respect of
> adding larger amount of molecules into the simulation box. is it
> possible that this "feature" will be fixed soon? are there any
> alternatives? adding molecules one-by-one (that seems to work ok) is not
> a solution for me, because i need to add many of them and this procedure
> doesn't leave enough space in the simulation box...
> thank you for any help. best regars,

I would suggest trying to start with an empty box, use genconf to put in
your molecules, then add water using genbox and finally run genbox again
to put a protein in the mixture.

David van der Spoel, PhD, Assoc. 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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