Thanks Jason!
I reran the simulation using identical parameters for 200 ps and collected
20 frames over this time.
Then I compared the overall r.m.s.d using ptraj of these 20 frames with the
20 frames of the original simulation (of 5ns). The r.m.s.d values shown in
the graph are for
1) first 20 frames of the original simulation and
2) 20 frames for the rerun of the simulation
with the same reference structure.
So can I say that the results from the original have been reproduced or do I
need to do a longer run of 5ns to
see if the results are identical/similar.
Thanks much!
Po
On Fri, Jul 22, 2011 at 8:03 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Jul 22, 2011 at 7:34 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
>
> > Dear All,
> >
> > I ran a molecular dynamics simulation of the exact same ligand-protein
> > complex, using the exact same parameters and input files ,twice. After
> > generating 20 frames (each) ,I calculated the rmsd (using ptraj) for each
> > and got the attached numbers.
> >
>
> 20 frames is ambiguous. Does that mean you ran the simulation for 20 steps
> and collected a snapshot each step? Was the total simulation 20 ps? The
> shorter the simulation, the less likely the simulations are identical if
> they've begun to diverge.
>
>
> > Can we say that the two simulations are identical, and that it has been
> > reproduced, based on these attached numbers?
> >
>
> Your RMSD values are not identical -- one is systematically smaller than
> the
> other. Furthermore, RMSD is not a sufficient metric to determine if 2
> simulations are identical (it can be enough, however, to declare that they
> are not). Consider what RMSD actually tells you: it tells you the average
> deviation of atomic positions. It says nothing about which direction the
> deviations occur in. Therefore, 2 structures with a 5 Angstrom RMSD from a
> common reference can be anywhere between 0 and 10 Angstroms deviation away
> from each other (over-simplified, of course, but you get the idea).
>
> However, were you even using the same reference in these 2 cases? (You
> should be).
>
> HTH,
> Jason
>
>
> > Thanks,
> >
> > Po
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 23 2011 - 06:00:03 PDT
