[gmx-users] The RMSD problem

[Qing Zhu]

For my understanding, what you said happens all the time. Because our 
simulation systems are very small and simulation time-scale is kind of 
short, system fluctuations and statistical errors may be big; even you 
run the simulations using the same initial conditions but only different 
random seeds, the simulation results could be significantly different. 
So my suggestion is run replicate simulation (5 or 6 might be enough), 
average the results, do statistical analysis, and find the real 
statistical average of your RMSD.

Good luck.

Qing Zhu

Tanping Li wrote:

>Dear all,
>
>Another problem bothering me for the
>protein(myoglobin) is the RMSD. Because it is a very
>compact protein made of 7 helices, so I expect the
>RMSD should be stable and low. I follow the steps EM,
>PR MD and full MD. But I still find out the RMSD is
>very sensitive. It converges to 0.15nm in one of the
>gound state I made, but if the initial condition is a
>little bit different, it converges to 0.25 sometimes.
>Could I believe that 0.15nm is the correct one and
>throw away the 0.25nm one? Where does this come from,
>force field or something else? Thank you very much to
>share your experience and view.
>
>
>
>Best
>Tanping
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