[gmx-users] cell exploding

[David van der Spoel]

On Mon, 2003-03-10 at 12:23, Yuguang Mu wrote:
> 
> > 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?
> 
> In my case, the RNA is intact, because I just want to equilibrate the
> water shell, and I freeze the RNA, only the water and ions can move.
> 
try without freezing. maybe there is some strain in your structure,
either due to conformation or due to forcefield
> 
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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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