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

From: Xi Chen (xichen930108_at_email.arizona.edu)
Date: Thu Jan 03 2019 - 20:17:29 CST

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
    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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