From: Xi Chen (xichen930108_at_email.arizona.edu)
Date: Fri Jan 04 2019 - 12:13:58 CST
Hi All:
I have been trying to run QM/MM simulation with NAMD-MOPAC, using PM7
method, on a small test system (one alanine in a square water box). As
described in full detail in another question posted previously, I kept
running into chemically incorrect simulation:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2018-2019/1389.html
I tried tuning keywords controlling the QM/MM simulation, and this
post is specifically for the wrong results I have when tuning the keyword
QMElecEmbed , which controls whether or not MOPAC will take classical point
charges into consideration for QM calculations.
As far as I know, MOPAC takes into account the classical point charges
by reading in a file called "mol.in", which should appear in the directory
specified in qmBaseDir. The trouble I have is that, I tried run two 0 step
(so that MOPAC is only invoked once by NAMD) simulations from the same
starting structure with QMElecEmbed set to on, and to off, separately,
but their "mol.in" file and result file ".aux" file were identical to each
other, meaning that tuning this keyword does not change anything to my
system. You can find my starting pdd, psf, topology files and output files
in this url:
http://schwartzgroup1.arizona.edu/~dimitri/ele.tar
In which, "mol.in_on" and ".aux_on" are results from the simulation
where QMElecEmbed is set to on, "mol.in_off" and ".aux_off" are results
from the simulation where QMElecEmbed is set to off. Unzip and run
ele.namd should be able to reproduce my result. Do check directories for
NAMD executable, MOPAC and qmBaseDir.
Any help will be appreciated. Thank you in advance!
Xi Chen
PhD Candidate, Schwartz Group
Department of Chemistry and Biochemistry
University of Arizona
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