[gmx-users] water molecule can not be settled, what could be the cause?
feenstra at few.vu.nl
Fri Jun 17 11:30:50 CEST 2005
Jian Zou wrote:
> David (if I'm right) ever said that this problem may be caused by that
> some water molecule is surrounded by hydrophobic surface, and starts to
> spin with a high velocity.
> Anton (if I'm right) ever made a comment that this high velocity is a
> physical phenomenon and is not well described by the MD because of the
> lack of energy transfer between the fast-moving water molecule and its
> surrounding environment.
> Is the problem as Anton described still unsolved by MD algorithms?
It may be physical, but it's almost certainly not interesting for most
Check which water molecule gives the problem, and see where it is in
relation to your protein.
As Tsjerk suggested, you can remove the water molecule if it's isolated
in the protein. It could also be near a charged residue on the protein
surface, in that case, you may get around by a bit more minimization
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