[gmx-developers] Incorrect simulation?
spoel at xray.bmc.uu.se
Fri Oct 14 22:54:36 CEST 2005
On Fri, 2005-10-14 at 15:34 -0400, Scott Thibault wrote:
> > -----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.
OK, but without solvent the Lennard-Jones forces will still make it
collapse. In SD you have the stochastic kicks that prevent complete
collapse. I'm a bit in the blue about the rationale of simulating
something like RNA without charges, since also HBonds will be repulsive.
Or do you mean without full charges?
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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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