On Fri, 2014-04-25 at 11:37 +0530, Arunima Shilpi wrote:
> Dear Sir
>
> Here in the command for MMPBSA/MMGBSA calculation following command has
> been used
>
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> ras-raf_solvated.prmtop
> -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd
> As per the tutorial instruction the production step was run 4 time for the
> analysis for 2ns.
The tutorial is a _demonstration_, not a prescription of best practices.
It is primarily concerned with helping you learn how to set up and run
calculations and analyze their results. Regarding the amount of
simulation you should run, you should run as much as you can given
resource constraints and then analyze as much of the simulation that is
"relevant" as possible.
Typically people omit pieces of the simulation in which you are heating
or stabilizing certain properties (like density, ion/solvent
distribution, native contacts, etc.) This phase is often termed
"equilibration" and is typically discarded in analysis. Everything else
is generally included.
With MM/PBSA analyses, the more data you have the better statistics that
you get. On the other hand, adding unphysical configurations will add
(unknown) systematic error to your calculation. So you want to use as
much of your simulation as you think is relevant to the equilibrium
properties of your system.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 25 2014 - 04:30:03 PDT
