mimicpy 0.3.0

Companion library to the MiMiC framework for input preparation.

MiMiCPy

MiMiCPy is the companion library to the MiMiC framework for streamline preparation of input files. It includes a suite of command line tools and plugins for PyMOL/VMD. Visit the MiMiC homepage for more details and documentation.

Requirements

Python

• Python >= 3.5, < 3.12 (Python 3.11 and below)

Core Dependencies

• pandas >= 0.24.0
• numpy >= 1.12.0

Force Matching Module

The force matching module requires additional dependencies:

• h5py >= 3.0.0
• MDAnalysis >= 2.0
• GROMACS (must be installed and accessible in the system PATH)

Optional

• PyMOL (for PrepQM plugin) - tested with version 2.3.4
• VMD (for PrepQM plugin) - tested with version 1.9.4a38

Installation

To install, run the following command:

pip install mimicpy

The PrepQM plugins for PyMOL and/or VMD can be optionally installed by running:

mimicpy_plugin_installer -pymoldir /path/to/plugin/ -vmddir /path/to/plugin/

The path to the plugin is usually either the path to the PyMOL/VMD installation, or the user home directory.

Demo

A demo of atom selection for the QM region, and generation of the MiMiC-based CPMD input file using MiMiCPy is shown below.

user@system:~$ mimicpy prepqm -top acetone.top -coords acetone.gro


 	                ***** MiMiCPy *****

 	 For more information type mimicpy [subcommand] --help

=====> Running prepqm <=====


**Reading topology**

Cannot find path to Gromacs installation.
Read atoms from acetone.itp.
No atoms found in acetone.top.

Some atom types had no atom numbers information.
They were guessed as follows:

+---------------------+
| Atom Type | Element |
+---------------------+
|     c     |    C    |
+---------------------+
|     c3    |    C    |
+---------------------+
|     o     |    O    |
+---------------------+
|     hc    |    H    |
+---------------------+

**Reading coordinates**  |Done

Please enter selection below. For more information type 'help'
> add resname is ACT
> q
Using default values for maxstep and timestep
Wrote Gromacs index file to index.ndx
Wrote new CPMD input script to cpmd.inp

=====> Done <=====

Force Matching

The force matching module in MiMiCPy automates the parameterization of molecular mechanics (MM) force field parameters by fitting to reference QM/MM data. It optimizes both non-bonded interactions (atomic charges via DRESP) and bonded interactions (bonds, angles, dihedrals) to reproduce QM forces and electrostatic properties.

Required Input Files

The force matching workflow requires the following input files:

• -top: GROMACS topology file (.top)
• -sele: QM region selection file (.txt or .dat) - specifies which atoms are in the QM region
• -fmdata: Force matching data file (.json or .h5) - contains QM/MM reference data (forces, charges, electrostatic potentials/fields)
• -fi: Force matching input file (.dat) - configuration file with optimization parameters
• -trr: GROMACS trajectory file (.trr) - trajectory from QM/MM simulation
• -ndx: GROMACS index file (.ndx) - atom index groups
• -coords: Coordinate file (.gro) - initial structure
• -mdp: GROMACS MDP file (.mdp, optional) - MD parameters for force recalculation

Basic Usage

The basic force matching command is:

mimicpy fm -top system.top -sele qm_selection.txt -fmdata fm_data.json -fi fm_input.inp -trr trajectory.trr -ndx index.ndx -coords system.gro -mdp run.mdp

Common Options

• -dresp: Run only DRESP charge optimization (skip bonded parameter optimization)
• -opt_ff: Run only force field parameter optimization (skip DRESP, uses existing charges)
• -grid_search: Perform grid search over DRESP weight parameters (wv, we, wh)
• -ff: Path to force field data directory (optional)
• -gmx: GROMACS executable name (default: gmx)
• -n_processes: Number of processes for parallel force computation