MoBioTools A simple yet versatile toolkit to automatically setup quantum mechanics/molecular mechanics

Overview

MoBioTools

A simple yet versatile toolkit to automatically setup quantum mechanics/molecular mechanics (QM/MM) calculations for ensembles of geometries generated from molecular dynamics trajectories.

Installation Requirements

A python installation with version >= 3.6 is required. Most Linux-based systems have a default python3 installation, otherwise one can use, e.g.: Anaconda (https://www.anaconda.com/products/individual), which includes more than 150 data analysis python libraries, or miniconda (https://docs.conda.io/en/latest/miniconda.html) which is a pocket version of anaconda that includes exclusively python. In either case, new libraries can be installed using the

conda

command.

Numpy: It comes with the anaconda distribution. Otherwise it can be installed via:

conda install numpy
pip install numpy

Cpptraj and pytraj:

If you have an Amber or an AmberTools installation, they should already be present in your $AMBERHOME amber installation directory. Otherwise, cpptraj needs to be installed first. To install pytraj, please visit https://amber-md.github.io/pytraj/latest/installation.html#install. To install cpptraj and pytraj from scratch, visit https://amber-md.github.io/pytraj/latest/installation.html#from-source-code-hard-way-expert-only.

Installation

Get the MoBioTools source

git clone [email protected]:mobiochem/MoBioTools.git

then, go to the MoBioTools directory

cd MoBioTools

set manually the environment variables in the config.sh script, then source it

source ./config.sh

and finally, carry out the installation itself

python3 setup.py install

Usage

The tools consist of two scripts with different functionalities:

  1. The input generator (main_qminputs.py, -h option to visualize the arguments it takes), which is compatible with the Gaussian, NWChem and (Open)Molcas quantum mechanics (QM) programs, takes an MD trajectory in amber format and generates an input file for all the snapshots selected by the user. The program takes two input files as arguments:
  • A main input file (-i option) on which the user defines the names of the trajectory file, the topology file, the desired QM program, the QM region to consider among others.

  • A template file, on which the specifics of the QM calulation are defined.

Some examples are provided on the examples/inputs folder.

cd examples/inputs

For example, in the case of a NWChem calculation, copy the trajectory and the topology files on the examples/inputs folder

cp GUA-O2-S5.* nwchem_input/.

cd nwchem_input

then execute the main_qminputs.py script as follows:

main_qminputs.py -i nwchem.main.in -t nwchem.tpl.inp
  1. The program to automaticall correct the active space of a set of CASSCF calculations an ensemble of geometries (pyoverlaps.py, -h option to visualize the arguments it takes).
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Comments
  • Bugfix

    Bugfix

    Output: Normal termination, remove gibberish A Topìsimo!

    Bug Report #################### DONE #################### Gaussian %chk #############################################

    #################### DONE #################### (Bugfix: Define one mainobj and one tplobj for each geometry iterated)

    range Issue: range of geometries arr0 = self._xyz[:, atm.indices]

    Range works when no bsse is used #############################################

    Output: switch mon1 and mon2 on the screen

    #################### DONE #################### Gaussian: No &basis &end for no gen; Parse gen on route

    generate a different namespace for %basis when using gen (gaussian) Remove directly the %basis from gaussian (?) #############################################

    NWChem

    #################### DONE #################### Solvent mask includes ions #############################################

    #################### DONE #################### bsse Molcas: Again closest funct. not working #############################################

    #################### DONE #################### solvmask needs to be initialized #############################################

    #################### DONE #################### chargers: xyz instead of dat #############################################

    opened by mobiochem 0
Owner
MoBioChem
The research group of Dr. Juanjo Nogueira at the Autonomous University of Madrid.
MoBioChem
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