Sonya,
> I have done molecular dynamics, explicit simulation
> of a short (8aa) alpha helix. I followed methods
> given by the tutorial. I am going to be comparing
> precise locations of backbone atoms in two such
> simulations. So, my concern is, how precise is the
> location of atoms in the simulation. I'm guessing
> that can't be answered w ith a simple number, but
> maybe you can tell me how I can figure out the
> answer from my simulation. Basically, i'm curious
> to what is the resolution of the result of my
> modeling.
If I understand right, you're saying you want to compare a particular
snapshot from simulation 1 with a particular snapshot from simulation
2, and draw conclusions based on the differences you see? This is
probably a very bad idea. MD does not give you a single structure --
not even in principle. Rather, you simulate the motion of the system;
in principle, if you simulate long enough, you'll sample from the
correct Boltzmann distribution of conformations. Maybe what you're
saying is that you want to compare the low energy conformations or low
free energy states from simulation (1) from those with simulation (2)?
I would resist the temptation to think of the end structure of one of
your MD simulations as the "result". It isn't. It's the final
structure (final snapshot), and is no more meaningful than any of the
other snapshots (after equilibration).
David Mobley
UCSF
On 2/12/07, Fenghui Fan <fenghui_fan.yahoo.com> wrote:
> In my opinion, maybe you cannot get a stable
> conformation. You can watch your simulation with VMD,
> and you can see the conformations change. From both
> the VMD and RMSD calculation, you can see there maybe
> several or even more conformations, and you can have
> each one for analysis.
>
> For analysis, will you please take a structure check
> tool for example Procheck? This will be very important
> to analysis your structure.
>
> I think these will be helpful.
>
> Best regards.
>
> Fenghui Fan
> --- "Dave, Sonya" <sonya.dave.vanderbilt.edu> wrote:
>
> > Hello,
> >
> > I have done molecular dynamics, explicit simulation
> > of a short (8aa) alpha helix. I followed methods
> > given by the tutorial. I am going to be comparing
> > precise locations of backbone atoms in two such
> > simulations. So, my concern is, how precise is the
> > location of atoms in the simulation. I'm guessing
> > that can't be answered w ith a simple number, but
> > maybe you can tell me how I can figure out the
> > answer from my simulation. Basically, i'm curious
> > to what is the resolution of the result of my
> > modeling.
> >
> > My guess is that I plot RMSd of the backbone atoms.
> > I usually do that just to make sure it has
> > stabilized. But, would the value of RMSd represent
> > the resolution?
> >
> > Another thing, I ran the simulation, and the final
> > product didn't really look like an alpha helix, it
> > was somewhat compressed/distorted. However, I
> > extracted the structure of the lowest potential
> > energy state (lowest EPTOT that was ever experienced
> > in the MD). That resembled a helix much more - But
> > still not perfect. So, obviously, in different
> > steps there is significant differences in geometry.
> > This concerns me, because I am concerned about small
> > distances here. So, how can I be fairly confident
> > my structure is the best structure?
> >
> > Thank you,
> > Sonya
> >
>
>
>
>
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Received on Wed Feb 14 2007 - 06:07:44 PST
