Dear Asmita,
See below my answers in red. I hope they help
Best
Vlad
On 12/02/2014 12:15 PM, Asmita Gupta wrote:
> 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.
I would advise to take both ... If your opening motion is an intrinsic
property of your system, ideally you would see reversible
opening/closing motions in your simulations. The more of those you see,
the more statistics of the transition you have. The more independent the
results are of your initial structure, the more confidence you gain in them.
>
> 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?
Personally, I would advise everybody to use the lambda approach
regardless of whether the system is mixed or not as it is more
straightforward to test different boost levels. However, some more
experienced people with aMD might see this differently ....
>
> 3. is it reasonable to collect snapshots at every 4-5ps, in aMD simulation
> (with 2fs integration, 200ns long run ??)
I guess this always depends on what type of motions you are looking for
and storage space available ... From your mail, I guess you are looking
after relatively slow motions, so 4-5 ps should be fine.
>
> Thanks
>
> Asmita
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>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Tue Dec 02 2014 - 05:00:02 PST
