[gmx-users] cell exploding

[Eric Jakobsson]

A possibly naive question, because I only know this stuff at a high 
level--it is the people in my lab who know the details:  When you freeze 
the RNA, does the RNA still interact electrostatically with the sodium 
ions?  If not, then you would have an enormous amount of positive charge in 
the sodium ions that would be repelling each other with no counter charge, 
would lead to the effect described.  To see, maybe try unfreezing the RNA.

Eric

At 04:59 PM 3/10/2003 +0100, you wrote:
>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
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909