Dear Fangma Ma,
I also want to know whether the periodic boundary conditions have any effect on the results in my reaction system? Do I need to use droplets in the QM/MM simulations of my reaction system?
It depends on the problem you are studying. The best is to test the effect for yourself. You can do this without requirement for major compute resources if you use a semiempirical method or DFTB. For a reaction that mostly depends on local electric fields I would not expect any significant effect. E.g. a free energy profile of a reaction in the center of a large water droplet or large bulk simulation box under periodic boundary conditions should yield equivalent results.
Note that, currently, when you use an ab initio or DFT method under periodic boundary conditions, then the QM/MM electrostatic coupling is truncated at the cutoff defined in the input file.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<http://www.awgoetz.de>
On May 7, 2021, at 1:48 AM, 马芳芳 <mafangfang0411.mail.dlut.edu.cn<mailto:mafangfang0411.mail.dlut.edu.cn>> wrote:
Dear Dr. Goetz,
Thanks for your kind help! I learned a lot. I also want to know whether the periodic boundary conditions have any effect on the results in my reaction system? Do I need to use droplets in the QM/MM simulations of my reaction system?
Best wishes and stay safe!
Fangfang Ma
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Received on Fri May 07 2021 - 12:30:02 PDT
