[gmx-users] Crush after ~135 ps

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 10 09:27:01 CEST 2003

On Thu, 2003-07-10 at 09:12, Semen Esilevsky wrote:
> > 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
> esceeded?
Settle crashes when the molecule moves more than a certain amount in a
single time step, e.g. for Lincs you would get a warning if a bond
vector rotates more then 30 degrees.
> > 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?
You can dump a timeframe from the trajectory in a .g96 file (has the
highest precision) and modify the velocities (to e.g. zero) and then use
this coordinate file for a continuation using grompp.

As far as I know this effect is an artefact due to a combination of
things. First since the water has very little interactions in a
hydrophobic environment (if that's correct) it will be free to move.
Secondly, any motion it has will be scaled by the temperature control
algorithm possibly making it worse. So there is no known solution. 

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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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