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HTMD Adaptive Sampling with OpenMM

A set of example scripts for running High Throughput Molecular Dynamics (HTMD) with Adaptive Sampling using OpenMM.

Getting Started

Prerequisites

HTMD is of course required, and is most easily installed through conda (described here). The scripts were tested with version 1.11.5, and may require adjustments for different versions.

Installing HTMD through conda will automatically install the other dependencies, namely OpenMM and MDTraj.

Code Structure

This repository has the following structure, matching the structure used for adaptive sampling, and assumes familiarity:

htmd-adaptive-openmm
│   README.md
│   generateOpenMMEquilibrated.sh - Generates equilibrated systems from initial_conditions and places them in generators.
│   openmm_equilibration.py - Runs the equilibration with OpenMM, using implicit solvent.
|   runAdaptiveMD.py - Runs HTMD Adaptive Sampling for the system prepared in generators.
└───initial_conditions
    │   2efv_second_attempt.pdb - Example initial conditions.  
└───generator_stuff
    │   openmm_adaptive_sim.py - Example OpenMM production script using implicit solvent
    │   run.sh - Job script called by HTMD that runs the production MD.
└───generators
    └───0
        |   input.coor - Initial input coordinates using AceMD coordinate file. 
        |   input.pdb - Initial input coordinates in PDB form.
        |   openmm_adaptive_sim.py - Copied from generator_stuff
        |   run.sh - Copied from generator_stuff. 
    └─── ...

Generating Initial Conditions

PDB files of your system with initial conditions to start sampling from should be placed in the folder initial_conditions. Included with the repo are initial conditions for studying slipknot formation in MJ0366.

The script generateOpenMMEquilibrated.sh can be used to take the starting structures in initial_conditions, run equilibration and copy all the required files for running adaptive sampling from the equilbrated system into folders within the folder generators:

./generateOpenMMEquilibrated.sh

The shell script calls the python script openmm_equilibration.py, which reads in the starting structures and equilibrates them using the Amber10 forcefield and Amber10 implicit solvent. This script should be modified as required for particular systems. It also copies the files in generator_stuff, which include the scripts required for production runs.

Running Adaptive Sampling

To run adaptive sampling after generating initial conditions, the script runAdaptiveMD.py can be used as a starting point.

python runAdaptiveMD.py

To modify the details of the production simulations run with adaptive sampling, edit the script generator_stuff/openmm_adaptive_sim.py.

Authors

License

This project is licensed under the MIT License - see the LICENSE.md file for details