[gmx-users] Water molecule near protein surface cannot be settled.

Dawid das addiw7 at googlemail.com
Mon Aug 11 11:32:40 CEST 2014

Dear Gromacs experts,

I have encountered quite annoying problem again. When I try either
minimization or NVT dynamics of my solvated protein system I get message
like this:

step -1: Water molecule starting at atom 16281 can not be settled.

It is for couple of water molecules. I have checked visually where these
molecules are and for minimization they are near surface of protein (not
buried inside). I attach the link for *gro, *top, *log and other files.
What can I do about it?


Best wishes,

Dawid Grabarek

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