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

Dawid das addiw7 at googlemail.com
Mon Aug 11 11:40:27 CEST 2014

I forgot to mention that I get similar error for steepest descent
minimization, not only conjugate gradient. Shall I change some options in
*mdp files?

2014-08-11 10:32 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> 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?
> http://www.speedyshare.com/rN4gx/mCherry7-min.tar.bz2
> http://www.speedyshare.com/BnwU5/mCherry7-nvt-md.tar.bz2
> http://www.speedyshare.com/3k9jz/charmm27-files.tar.bz2
> Best wishes,
> Dawid Grabarek

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