Installation

install mambaforge or miniforge

install numpy, scipy, and ipython

you should now have seperate directroy with qmhub.ini, qmmm.inp, and qmmm.out

you run qmhub in this directory .. code-block:

qmhub -t qmmm.inp qmhub.ini

Outside of this directory, run the following commands: .. code-block:

git clone https://github.com/andysim/helpme.git
cd helpme
module load CMake/3.9.6
mkdir build
cp cmake.sh build
cd build
bash cmake.sh
make helpmelib
cp python/helpmelib.cpython-310-x86_64-linux-gnu.so /[pwd]/mambaforge/lib/[python.version]/site-packages/qmhub

N.B. you have your own cmake.sh for your server enviorment, for example:

if you use an intel compilers, you will need to compile each time at the start of the session; run:

..code-block::

module load intel/2020a export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_core.so:$MKLROOT/lib/intel64/libmkl_sequential.so

If errors are encountered, see: https://stackoverflow.com/questions/61341878/intel-mkl-fatal-error-when-running-kaldi-gst-live-demo

Command Line Usage

Generate the .inp input file manually

use mdanaylsis, a script with protein databank file, or anything that can generate data in right format

https://docs.mdanalysis.org/stable/index.html

qmmm.inp contains:

first 3 columns xyz cordiantes

4th column is charge for MM

5th column is atomic number for QM

run: .. code-block:

qmhub -t qmmm.inp qmhub.ini

View the output in qmmm.out as a coordinate list

N.B. in qmmm.ini, nrespa is the number of MM cycles between QM cycles

Python Module

qmhub can be used as a python moduele that can do all and more of qmhub commandline functionality:

take arrays from .nc and .psf formate and copy them directly into QMhub with protein data bank files, mdanaylsis, anything

force matching

Maxmimum likelihood potentional training

energy weighting

by using python to extract the desired array from qmhub and do maniputations or seperate from simulations