[gmx-developers] Incorrect simulation?

[David]

On Fri, 2005-10-14 at 14:54 -0400, Scott Thibault wrote:
> > On Fri, 2005-10-14 at 12:13 -0400, Scott Thibault wrote:
> > > I'm trying to simulate an RNA molecule and it seems to 
> > simulate normal 
> > > with the sd integrator, but if I just change that one 
> > parameter to md 
> > > the results are incorrect.  The molecule quickly (<100,000 steps) 
> > > collapses into a nested ball.  Any ideas what is happening here?
> > 
> > Do you have solvent?
> 
> No, its in a vacuum.
Then that explains it. How about the charges on the backbone?

> 
> --Scott
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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