AMBER Archive (2007)

Subject: AMBER: How precise is a MD simulation?

From: Dave, Sonya (sonya.dave_at_vanderbilt.edu)
Date: Mon Feb 12 2007 - 18:00:07 CST

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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