[gmx-developers] Incorrect simulation?

[Scott Thibault]

> > > > > > 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?

It looks like you were right, the model is designed to rely on the
stochastic kicks for solvent-like behavior.  Good call.

I'm looking for something to simulate in a vaccum (i.e. not a lot of
atoms) that has some visual aspect that is easy to see by the general
public for a demo.  The tRNA example is good, but the sd integrator
might be hard to implement.

Thanks for the help,
--Scott