[gmx-users] Crush after ~135 ps

Semen Esilevsky yesint4 at yahoo.com
Thu Jul 10 09:13:01 CEST 2003

> one possibility is that a water molecule is trapped
> in a hydrophobic
> environment without hydrogen bonds. Then it may
> start spinning and the
> Settle error can occur. This is usually quite hard
> to find out because
> you need to know the velocity of the molecule. If
> you know which water
> it is (written in the log file) you can try to
> animate the trajectory.

Yes, I know which molecule is responsible for crush,
but what is a velocity criterion which shouldn't be
> Assigning new velocities and/or continuing the
> trajectory from, say, 100
> ps might be enough to get over this problem.

How to assign new velocity for a given water? 
As I understand this situation may appear again
unpredictably. Is it possible to get rid of it once
and forever?

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