Re: [AMBER] Problem related to the umbrella sampling

From: Jason Swails <>
Date: Fri, 12 Jul 2013 00:37:29 -0400

On Jul 12, 2013, at 12:23 AM, Sindrila Dutta banik <> wrote:

> Thanks once again.
> One article is attached (JACS, 2006, 128, 16345) where they compute PMF classically and compare it with QM. Can I do similar study using Amber, if yes then how?

I think you are misunderstanding what they are doing in that paper. They never claim to use just classical mechanics. They use QM/MM, where the reaction center is treated with a QM Hamiltonian.

They appear to compare low-level QMMM with higher level QM ( AM1 vs. DFT), although I did not read the paper that carefully. However, they never try to break and make bonds inside the force field (since this is impossible).

To answer your question about whether amber can do a similar study to the one that was done, the answer is yes.


Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Jul 11 2013 - 22:00:03 PDT
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