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

[Dawid das]

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
>