Date: Tue, 8 Mar 2016 14:06:10 -0500
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.
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?
Sorry to put up these simple questions but if anybody could give some
response/suggestions, it would be really helpful.
(First few frames)
#Frame RMSD_00001
0.2 0.6366
0.4 0.6494
0.6 0.6472
0.8 0.6625
1 0.6608
1.2 0.665
[image: Inline image 1]
Thanks in advance for your valuable time.
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