[gmx-users] Crush after ~135 ps
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
Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month!
More information about the gromacs.org_gmx-users