[gmx-users] create a sphere of water molecules

Erik Marklund erikm at xray.bmc.uu.se
Wed Apr 13 15:48:23 CEST 2011

Olga Ivchenko skrev 2011-04-13 15.20:
> Dear Gromacs Users,
> I want to add a sphere of water molecules around a ligand. I know I 
> need to use -shell option in genbox. But first I I need to create a 
> sphere. Please could you guide me?
> best,
> Olga
Just fill the box with water, then run trjorder to sort the solvent 
according to their distance to the ligand. Having done that, you can 
just edit away the bottom part of the sorted gro-file to have your 
ligand in a ball of water.

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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