AMBER Archive (2006)

Subject: Re: AMBER: Unstable RMS trajectory

From: Gustavo Seabra (
Date: Tue Oct 17 2006 - 11:22:31 CDT

Would you not expect the vacuum structure to be different than the
solvated one? Assuming it is not an error, I think we should expect
the RMSD to increase as you go from the vacuum to the solvated

However, a movie would still be the best way to tell. The only problem
is that, as I understand, this is a minimization, right? How can she
generate a movie from the minimization? (I tried it before, but my
mdcrd files came up empty...)


On 10/17/06, Carlos Simmerling <> wrote:
> I think it is always a good idea to visually inspect the
> trajectories and not to just trust rmsd values or other
> numerical measures since there could always be a problem
> in your analysis scripts.
> Dave, Sonya wrote:
> > Hi,
> >
> > I am minimizing a protein in water, using explicit solvent. I'm
> > following the input files of the tutorial 1, part 3/4. Except, i am
> > applying it to a protein.
> >
> > The vacuum minimization works fine, in that RMS stabilizes and EP tot
> > decreases and stabilizes. However, for the water explicit
> > minimizations, the RMS shoots off to high values, in a smooth
> > continually increasing fashion. I am using the result of vacuum
> > simulation PDB as the input for all my water simulations (i am first
> > fixing the protein, the removing restraints, per the tutorial).
> >
> > I am plotting potential energy and RMS during the simulation. The PE
> > initially spiked up, but now it's is decreasing and stabilizing (at a
> > highly negative value). The RMS, however, continues to rise.
> >
> > Does this always mean there is something wrong with my simulation? Or
> > do I have to make movies of the files to be sure? If it means
> > something is wrong, how do i decide what to change to make it right?
> >
> > Thank you,
> > Sonya Dave'
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