[gmx-users] Water molecule can not be settled

[David van der Spoel]

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 ps):
> 
> 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...


> 
> Thanks in advance for any help
> 
> 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
> 
> 
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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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