[gmx-users] cell exploding

[David van der Spoel]

On Mon, 2003-03-10 at 12:07, Yuguang Mu wrote:
> I have checked  energy as a function of time,
> they seems OK.
> The density decreases greatly as the box explods
> 
> The pressure has strange behavior, after initio drops, it stay on a
> platform, around 1000 bar, and fluctuats there.

Is your RNA intact?


> 
> I think this is the reason why box explods, the pressure is
> always maintaining  on a high level.
> 
> But how come ?
> 
> My system is neutral RNA (-22) with 22 Na+ counterions.
> 
> 
> > On Mon, 2003-03-10 at 11:50, Yuguang Mu wrote:
> > > I even try tau_p = 10 ps
> > > It still explods
> > check density and energy as a function of time (even energy components).
> > Do you have net charge on the system?
> >
> > More details please!
> > >
> > >
> > > > On Mon, 2003-03-10 at 10:32, Yuguang Mu wrote:
> > > > > Hi Gmx-users,
> > > > > My simulation system is RNA + water + Na+
> > > > > If I did it without pressure coupling, the simulation is quite OK.
> > > > > But when I switch on the pressure coupling,
> > > > > the box begins exploding then crash after around 100 ps.
> > > > >
> > > > > Do you know some reasons ?
> > > > maybe too tight p coupling. Set tau_p to 1 ps.
> > > >
> > >
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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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-- 
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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