Re: AMBER: How precise is a MD simulation?

From: Fenghui Fan <>
Date: Mon, 12 Feb 2007 17:47:09 -0800 (PST)

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" <> 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 - 06:07:32 PST
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