[gmx-users] re: Crush after ~135 ps

[Yuguang Mu]

I also encountered such problems in my simulation of some
modified molecules.
I decided to give up the restrains, and using flexible water model,
of course the simulation time step had to be reduced to 1 fs.
It seems work, but slower.

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On 10 Jul 2003, David van der Spoel wrote:

> 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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