[gmx-developers] Incorrect simulation?
thibault at gmvhdl.com
Fri Oct 14 21:34:17 CEST 2005
> -----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.
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