Re: Wrong result in running QM/MM simulation with a small test system

From: Marcelo C. R. Melo (
Date: Mon Jan 07 2019 - 12:55:52 CST

Hi, Xi,
You have to remember that the calculation is doing the best it can in the
context you created. You put one (1) amino acid in a QM region surrounded
by constant partial charges from the classical water molecules. Expecting
that to give a perfect account of the real system would be unreasonable.
All sorts of characteristics could be *very* distant from reality, like
charge distribution or geometry. If you want to study the (de)protonation,
you should at least add a few shells of water molecules around the QM
QM/MM is a trade-off between cost and precision. You turned the dial all
the way to minimum cost.

Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
+1 (217) 244-5983
On Thu, 3 Jan 2019 at 20:19, Xi Chen <> wrote:
> Hi All:
>     I have been trying to run QM/MM  simulation on a small test system
> (one alanine molecule in a square water box) with NAMD-MOPAC, using PM7
> method. The system does not contain any other molecules besides the alanine
> and water molecules, so it should be close to neutral pH. Therefore, I set
> the starting structure of the alanine molecule to be in its zwitterinonic
> form (NH3+ and COO-). However, a QM/MM simulation with this starting
> structure, using PM7  method, would results in one of the hydrogen atom on
> the amine group being inventively transferred to the carboxyl group, and
> results in a not ionized structure (NH2, COOH), which is not chemically
> correct.
>     I tried changing simulation set up, like cut off distance, QM
> switching, etc, but none worked. Not sure if this happen because my input
> file has a mistake, or it's something else.
>     Use this url to download the starting psf, pdb and input file for my
> system:
>     Unzip the PM7.tar file and run PM7.namd (a 1000 steps QM/MM
> simulation) should be able to reproduce my results. Do chekc PM7.namd, and
> make sure the directories for NAMD executable, MOPAC and qmBaseDir meet
> with the directories in your machine.
>     Any help would be appreciated.Thank you in advance!
> Xi Chen
> PhD Candidate, Schwartz Group
> Department of Chemistry and Biochemistry
> University of Arizona

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