[gmx-developers] Incorrect simulation?

[Scott Thibault]

> -----Original Message-----
> From: gmx-developers-bounces at gromacs.org 
> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of David
> Sent: Friday, October 14, 2005 3:05 PM
> To: Discussion list for GROMACS development
> Subject: RE: [gmx-developers] Incorrect simulation?
> 
> 
> 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?

I'm using a model from http://folding.stanford.edu/tRNA/.  Atom charges
are all 0.

--Scott