Thanks Vlad, for the quick responses. Yes the overall movement is slow and
besides, the system is big, so collecting frames at every 1 or 2 ps results
in huge crd files.
On Tue, Dec 2, 2014 at 6:02 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> 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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>
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Received on Tue Dec 02 2014 - 08:00:02 PST
