From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Mon Jan 07 2019 - 12:55:52 CST
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 crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Thu, 3 Jan 2019 at 20:19, Xi Chen <xichen930108_at_email.arizona.edu> 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: > http://schwartzgroup1.arizona.edu/~dimitri/PM7.tar > 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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