Dear all,
Since tutorials are starting to be old a bit, I was wondering what could
be a reasonable time for computing
MM/GBSA - PBSA in a long simulation time.
In fact I performed various 2 to 5 µs simulations and I want to compare
them, and while monitoring their energy over time,
I find some changes and plateaus for long period (500ns to 1µs) and of
course some changes due to the protein evolution
relative to the membrane.
Since in early paper (ras-raf) the simulation time was around 10ns, I
wondered if it was better to do subsampling of the trajectories
(for instance in 3/4 plateau) or even it the simulation is 5µs, the time
is still considered very small so there is no need to subsample
the trajectory since we are still in the "small change in entropy zone".
Thanks a lot for your answers and/or link to literature I may have missed.
Stéphane
--
Assistant Professor, USBB, UMR 6286 CNRS, Bioinformatique Structurale
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.us2b.univ-nantes.fr/ -http://www.steletch.org
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Received on Wed Jul 03 2024 - 02:00:02 PDT
