Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian.

From: Bill Ross <>
Date: Mon, 17 Aug 2015 13:09:34 -0700

During dynamics higher-energy conformations are reached than minimized at 0 K. You are worried about the magnitude of the differences, but it would also be interesting to see what energies Amber gives for the minimized monomers with your parameters. This would be a check on your parameterization.


<div>-------- Original message --------</div><div>From: Eg eh <> </div><div>Date:08/17/2015 12:08 PM (GMT-08:00) </div><div>To: </div><div>Subject: [AMBER] Big potential difference between conformation in MD
  simulation and optimized conformation in Gaussian. </div><div>
</div>Dear all,
I am doing simulation with a polymer in TIP3P water now. The monomer has a 7membered ring. I used PARAMFIT to get a set of force field for it. I used TLEAP to combine monomers to a polymer and pack it with TIP3P water.
After running for 20ns (NPT), I extracted some fragment from the trajectory file. These fragments were all monomer with missing terminals. I added hydrogen atoms to makeup the terminals. And then I used Gaussian09 to do SP and OPT with MP2/6-31G* to see the potential difference.
The results showed the conformation extracted from MD simulation had much higher potential than its optimized conformation. I had 24 conformations. The biggest potential difference was 66kcal/mol. The smallest potential difference was 35kcal/mol.
I know AMBER could overcome small energy barrier, but the potential difference was too big. Is this condition normal?

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Received on Mon Aug 17 2015 - 13:30:04 PDT
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