[gmx-users] Water molecule can not be settled

[Ester Chiessi]

Anton Feenstra wrote:

> David van der Spoel wrote:
> > On Mon, 2003-03-17 at 14:15, Ester Chiessi wrote:
> >
> >>Dear all,
> >>
> >>I was equilibrating my system (a polymer in a water box, at 303 K ) and the total
> >>energy drift was decreasing as expected.
> >>After about 50 ps of MD, my calculation stopped with the following message (the
> >>timestep was 1 fs):
> >>
> >>t = 48.064 ps: Water molecule starting at atom 1865 can not be settled.
> >>Check for bad contacts and/or reduce the timestep.Fatal error:
> >>t = 48.064 ps: Water molecule starting at atom 1865 can not be settled.
> >>Check for bad contacts and/or reduce the timestep.
> >>
> >>I verified a short contact between atoms of two water molecoles, not
> >>involved in the hydration shell of the solute.
> >>
> >>How may I go on?
> >
> >
> > this usually happens when you have one water without hydrogen bonds
> > (i.e. in vacuum, or a completely hydrophobic surrounding), that starts
> > spinning for whatever reason. You may indeed reduce the timestep, or
> > otherwise regenerate velocities (with grompp). In both cases your
> > trajectory will become discontinuous...
>
> Alternately, you might 'tweak' your simulation a bit upstream. What
> I mean is this: the chance of this water molecule starting to spin
> so fast is very small. If you would take for example your last .trr
> frame (x+v for restart) at a few ps before the crash, and introduce
> slight rounding errors in the 6th decimal place for coordinates and
> trajectories
> using "trjconv -s topol.tpr -f traj.trr -ndec 6 -dump 45 -o frame.gro"
> and "trjconv -f frame.gro -o frame.trr"
> and "tpbconv -s topol.tpr -f frame.trr -o new.tpr"
> you will have a nearly continuous trajectory (single precision is
> only 7 decimal places, you round at 6), but the chance of getting that
> same water to spin again is virtually zero.

Thanks for your suggestions.

But couldn't  this anomalous behavior of a water molecule suggest some heavy mistake
in the model?
Which controls may I performe to avoid a similar event in another point of my
trajectory?

I verified that the 'incriminated' water is 4.11 angstrom far from the nearest atom of
the solute ( a quite hydrophilic polymer ), in the pdb of the last completed step.
This water is in the proximity of a face of the box.

Hi, Ester

--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328