Welcome to gmx2qmmm

gmx2qmmm is a python interface for Quantum mechanics/Molecular mechanics (QM/MM) calculation.

Overview

gmx2qmmm is a python package to bridge Gaussian and Gromacs. The test runs were performed using Gaussian16 and Gromacs 5.0.2, but the code should be able to read earlier Gaussian and other Gromacs versions. The only limits are the formats of the human-readable input and output files of each program, as such, conversion scripts can be written to make the interface work with any version, if the current code does not support it. Conceptually, gmx2qmmm creates a QM/MM potential and performs either single point calculations (i.e., the current energy of your system), geometry optimizations, and linear relaxed scan. (Other ultilities are ongoing)

System requirements

• python 3.6+
• Gaussian16 (and earlier version)
• Gromacs 5.0.2 (and earlier version)

Downloads

• Download in Git manually

• git clone

     git clone --branch p3	https://github.com/gmx2qmmm/gmx2qmmm_portable.git
  

gmx2qmmm jobs

Job type	Calculation
Single point calcuation (SP)	Calculate single point energy and forces
Geometry optimizations (OPT)	Optimize the system energy via optimizer (Steepest descent, Conjugate gradient or BFGS)
Relaxed Scan (SCAN)	Relaxed linear scan (angle and dihedral angle are in development)

If the calculation is interupted at some point, please check Continue the calculation to continue.

gmx2qmmm input files

usage: gmx2qmmm.py [-h] [-c COORD] [-p TOP] [-n QMATOMS] [-qm QMFILE][-mm MMFILE] [-qmmm QMMMFILE] [-act ACT] [-path PATHFILE] [-g LOGFILE]

see details

Input files	Command	Default input name
Coordinate file (.g96 or .gro)	-c	conf.g96
Topology (.top)	-p	topol.top
QM atoms file (.ndx)	-n	qmatoms.ndx
QM parameters (.dat)	-qm	qm.dat
MM parameters (.dat)	-mm	mm.dat
QM/MM parameters (.dat)	-qmmm	qmmm.dat
Active atoms (.ndx)	-act	act.ndx
Path file (.dat)	-path	path.dat
Logfile (.log)	-g	logfile

gmx2qmmm output files

• Single point calcuation (SP)

  	File name	Description
  Energy	oenergy.txt	QM, MM, Link and Total Energy
  Forces	oforces.txt	X,Y,Z Forces at each atom

• Geometry optimizations (OPT)

  	File name	Description
  Energy	oenergy.txt	QM, MM, Link and Total Energy in each step
  Forces	oforces.txt	X,Y,Z Forces at each atom in each step

  • Set print_level=NORMAL in -qmmm file : Remain the last step information only
  • Set print_level=FULL in -qmmm file : Remain all information

• Relaxed Scan (SCAN)

  	File name	Description
  Energy	oenergy.txt	QM, MM, Link and Total Energy in each scan step
  Forces	oforces.txt	X,Y,Z Forces at each atom in each scan step
  Energy	oenergy_scanRa-b_step.txt	print_level=FULL in -qmmm file is required. QM, MM, Link and Total Energy every OPT step in each scan step. a,b:scan atom
  Forces	oforces_scanRa-b_step.txt	print_level=FULL in -qmmm file is required. X,Y,Z Forces at each atom every OPT step in each scan step. a,b:scan atom

  Since there are many output files in the scan job, the output files are store in a subdirectory of the base directory. 

  • Example: Linear scan atom1 and atom2 by 3 steps with print_level=NORMAL

      base_directory/
      |-- scanR/
      |--R1-2/ (contains last OPT output)
      |-- oenergy.txt (Scan energies)
      |-- oforces.txt (Scan Forces)
      ...
    

  • Example: Linear scan atom1 and atom2 by 3 steps with print_level=FULL

      base_directory/
      |-- scanR/
      |--R1-2/ (contains all OPT output)
      |-- oenergy.txt (Scan energies)
      |-- oforces.txt (Scan Forces)
      |-- oenergy_scanR1-2_1.txt (OPT energies in scan step 1)
      |-- oenergy_scanR1-2_2.txt (OPT energies in scan step 2)
      |-- oenergy_scanR1-2_3.txt (OPT energies in scan step 3)
      |-- oforces_scanR1-2_1.txt (OPT forces in scan step 1)
      |-- oforces_scanR1-2_2.txt (OPT forces in scan step 2)
      |-- oforces_scanR1-2_3.txt (OPT forces in scan step 3)
      ...
    

Startup examples : glycine serine

The turtorial contains SP and OPT calculation of glycine serine (GLYSER).

See the tutorial

References

A user‐friendly, Python‐based quantum mechanics/Gromacs interface: gmx2qmmm Jan P. Götze, Yuan‐Wei Pi, Simon Petry, Fabian Langkabel, Jan Felix Witte, Oliver Lemke https://doi.org/10.1002/qua.26486

Support and development

For bug reports/suggestions/complaints please raise an issue on GitHub.

Or contact us directly: gmx2qmmm@gmail.com