Dear David and Sonya,
I face the same problem as well. I run a 200ps+1ns simulations in implicit
(GB) solvent models. I noted that the potential energy and overall rmsd
become constant after ~ 200 ps. Just I assume it is equilibriated
afterwards. However, when I closly look at the structure after the first
200 ps, I noted that one of the torisonal angles at the active site is
decreasing from 10 degrees to 1 degree.
I agree that I should not just report the final structure. However, if I
report the torisonal angles keep changing after ~200ps, Can I still say the
structures after 200ps is equilbrated? Could you teach me which structure
should I report?
Best regards and many thanks in advanced,
Catherine
>From: "David Mobley" <dmobley.gmail.com>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: How precise is a MD simulation?
>Date: Tue, 13 Feb 2007 12:19:13 -0800
>
>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 - 06:07:48 PST
