On Tue, Apr 28, 2015 at 3:40 PM, Laura Tociu <ltociu.princeton.edu> wrote:
> Thank you both!
>
> Yes, I was saving frames every 20 femtoseconds in order to obtain that many
> frames (I had 5 ns of equilibrated trajectory I wanted to use). It seems
> like that is bad because the frames are not decorrelated.
Exactly. Two correlated snapshots contain significantly less information
than two independent ones.
>
> What exactly is a
>
> good time step for entropy calculation? Around 1 ps?
>
It's a compromise. The longer the better as far as ensuring that whatever
property you're measuring will have a correlation time shorter than the
sampling interval. But if you wait *too* long, and your simulation is too
short, then you lose potentially helpful information.
So the answer likely depends on how long you plan on running (or how long
you can afford to run). I typically sample around 1 to 2 ps. Other
colleagues sample more like every 10 ps (or maybe longer?) -- but they run
longer simulations than I do.
One more question: If I use only the alpha carbons, what do I do with the
> ligand, which is free arginine? If I represent it just by one atom, its
> alpha atom, it seems a little weird. Should I include all of the arginine's
> atoms both in the compex trajectory and the arginine trajectory? Or does it
> not make a big difference what I do with the arginine since its entropy
> will be small compared to that of the complex and receptor?
>
Are you using a single- or multiple-trajectory approach here? If you use
the single-trajectory approach, ignoring the ligand will be pointless --
the complex and receptor will then be identical and your entropy
contributions will be exactly zero.
You could clip your system to the entire ligand + receptor alpha carbons
and see how that fares. You could also simulate the free receptor and do a
multiple-trajectory approach to compute the binding entropy, and ignore the
ligand (you could always add a correction assuming the ligand was rigid and
compute just the rotational and translational entropy)...
I'm not sure what the best approach would be. The paper Josh mentioned is
probably worth a read to see what they suggest.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 28 2015 - 19:00:02 PDT
