Sonya,
> Thank you David. That makes sense that you say the final structure is no
> different from others. To clarify, I will be comparing lowest energy
> structures from simulations of two different molecules. I want to see what
> is the differences in those structures.
Is this in explicit solvent? Solvent degrees of freedom tend to add
large fluctuations to the total energy, meaning that the lowest energy
structure you find may be the lowest energy structure not because of
the protein/biomolecule structure, but because the solvent adopted a
particularly favorable conformation.
> So, what I'm going to do is pull out several of the lowest energy
> structures from each simulation. Then, I will see if the differences in
> frames of one simulation are significant compared to the differences in
> between the two molecules.
The key word here is "significant". Maybe you want to think of doing
sort of an error analysis -- block your simulation up into chunks (or
run several simulations); repeat your analysis separately for each
separate simulation and make sure your results are robust across
simulations or blocks.
Part of the potential problem can be that there are a lot of
"irrelevant" differences that can make big differences in potential
energies -- for example, a tiny shift of one atom (a fraction of an
angstrom) when it is making close contacts with another can cause the
potential energy to change wildly. What you want to make sure is that
the differences you see between the low potential energy structures
are actually meaningful, not just concidental.
David
> Thanks,
> Sonya
>
> -----Original Message-----
> From: owner-amber.scripps.edu on behalf of David Mobley
> Sent: Tue 2/13/2007 1:36 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: How precise is a MD simulation?
>
> 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
