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
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jul 22 2011 - 08:00:03 PDT
