[gmx-developers] Incorrect simulation?

[Scott Thibault]

> > > 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?

I've been talking to the group at Stanford that developed the model, and
I guess there is something special about the model so they don't need a
solvent.  I'll see if they can help me figure it out, since they know
more about the model.

Thanks,
--Scott