Not using SHAKE for the solute intramolecular hydrogen bonds may be okay
by using a small time step, 1 fs or less; but what about with TIP3P
waters. Wasn't the TIP3P water model designed on the basis of a
restrained geometry, namely using SHAKE? I assume that the DNA is
solvated in the simulation.
I would be curious as to any comments on this matter?
Troy Wymore
Biomedical Initiative Group
Pittsburgh Supercomputing Center
On Tue, 27 Feb 2001, Bill Ross wrote:
> I was thinking in terms of the longest timestep one could
> get away with; Jim Caldwell's .25 fs may be particularly
> worth trying if accurate H stretching is desired for
> calculating electron affinities per the original question.
>
> Bill Ross
>
>
> Strictly speaking it should be 0.25fs, you can try
> longer steps but watch your simulation carefully
> for instability.
>
> jim
>
> On Mon, 26 Feb 2001, Bill Ross wrote:
>
> > My question is, can I run MD for solvated DNA with SHAKE
> > turned off? What settings should I use to make sure the
> > simulation runs smoothly?
> >
> > Timestep = 1 fs instead of 2 is the common practise, I believe.
> >
> > Bill Ross
> >
>
>
Received on Wed Feb 28 2001 - 10:59:51 PST
