[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Jochen Hub jochen at xray.bmc.uu.se
Sun Apr 18 10:47:56 CEST 2010

rasoul nasiri wrote:
> Dear All,
> Hello
> I understand one can adjust distance of between solvent molecules by 
> genbox command and -vdwd  but I don't know, how do it between the 
> solutes?
If you want to place several identical solutes with genbox -ci, then you 
could copy the file vdwradii.dat to the present directory and largely 
increase the respective vdw radii in that file (e.g. the carbon radii) 
before running genbox.



> Thanks for helping!
> Rasoul

Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

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