On 5/17/12 10:38 AM, Steven Neumann wrote:
Well, I am still getting the same error when I try to do minimization: "water
molecule on atom X cannot be settled" - these water molecules are not close to
the Tube surface. If I will remove them the same error will occur but on the
other atoms. If I specified only vdwradii for my Tube atoms why in the bulk of
water there are some overlaps? Can you please help?
The problem is not necessarily with the water molecule, but is more often
indicative of some other instability in the system, such that forces are
transmitted to that poor unsuspecting water molecule and it blows up.
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
It's hard to diagnose, so make sure you're EM step is very small and you save
configurations frequently in order to diagnose what's happening. It could be a
problem with the .mdp file, topology, or perhaps some weird water overlap, but
if that's the case, then genbox didn't do it, something else caused it.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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