[gmx-users] clashes

Dariush Mohammadyani d.mohammadyani at gmail.com
Wed Mar 14 15:03:31 CET 2012

Dear user,

When I am using:
genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro

to add water in a coarse grained system, after running mdrun I am getting
"Syntax error" and it shows maybe the distances are so close or there are
some clashes.

Do you know how can I figure it out?
Or actually if we have some clashes in system how we can correct them?

Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
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