On Tue, Mar 8, 2016 at 2:06 PM, Arati Paudyal <apsilwal123.gmail.com> wrote:
> Dear all,
>
> I just finished the tutorial for MMPB/GB SA with ras-raf protein and I
> followed the tutorial. But this time I ran the the equilibrium step for
> 30,000,000 steps for a total simulation time of 60 ns instead of 500 ps as
> in tutorial. In the tutorial, there are separate production steps run for a
> total of 2 ns. I guess, my questions is, if you run your equilibiation
> phase for 60 ps already, do I need to run the production step again? I
> checked everything including rmsd, energy and density and my system is
> fully equilibriated.
>
There is really no difference between "equilibration" and "production" in
terms of simulation protocol. "Equilibration" is simply what we call the
portion of the production simulation in the beginning that we discard
because there is a high(er) likelihood that it is not sampling from an
equilibrium distribution.
So if you ran 60 ns of MD, and you think that (for whatever justification),
the last 58 ns sample from the free energy surface (i.e., the equilibrium
distribution), then you should start your MMPBSA.py analyses from the start
of the 3rd nanosecond.
If NOT, then when we run the mmpbsa.py script, how do we start from the
> point where the system is already equilibriated? Is it something do do with
> the start and end frames in the script? For eg. following is the rmsd plot
> of my system afte 60ns of equilibriation. I can see the system is
> equilibriated after about 200 frames. So can I assign my start frame as 200
> and end frame as 700?
>
I would suggest setting your start frame to 200 or so, as you said, and
then putting your endframe to the very end of the simulation. You can pick
a long interval to reduce the number of structures you feed to MMPBSA.py.
The more time between adjacent snapshots, the less correlated the results
will be (and therefore, the more statistically significant they will be).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 08 2016 - 19:00:03 PST
