[gmx-users] Water molecule cannot be settled

Steven Neumann s.neumann08 at gmail.com
Thu May 17 10:26:46 CEST 2012

Dear Gmx Users,

My system consists of a tube which is representated by atoms which are not
connected via bonds. The terminals of the tube are on the edge of the box.
I try to run minimization and get an error of many "water molecule cannot
be settled". I observed EM with nstxout = 1 and using VMD I observed that
mentioned water atoms collide with NA ions. These water molecules are not
trapped inside of my tube but outside. Why gromacs put water molecules like
this and by replacement of ions these collisions appear? Do you have any
solution for this?

Another thing: How can I select all the atoms inside my tube? I know
g_select but no clue how to define criteria.

Thank you,

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