Dear users,
I have run a 150ns conventional unbiased MD simulation to study
structural dynamics of a protein. With waters and ions included, the total
system size is 1,70,400 atoms. The protein displays an opening movement
within initial 100ns itself. Now, the experimental kinetic data that could
justify the opening within this short time scale is not available (reason
why i did md in the first place), i would like 2 set up 2 replicate
independent simulations for the same system. I have following doubts:-
1. If i want to reproduce the movement using accelerated MD, should i take
the starting structure from the end of cMD simulation or from the end of
equilibration phase (i.e. just before starting cMD) ?? In this paper,
authors have used former approach
http://www.pnas.org/content/110/27/10982.long#sec-1 ; while in amber
tutorials it is the other way.
2. In the same paper, the parameters for aMD are derived using the lambda
approach, because system is not homogenous (lipds + proteins), while in
tutorials a different approach is used. My system is all proteins, so can i
go with the tutorial formula to calculate aMD parameters?
3. is it reasonable to collect snapshots at every 4-5ps, in aMD simulation
(with 2fs integration, 200ns long run ??)
Thanks
Asmita
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Received on Tue Dec 02 2014 - 03:30:02 PST
