gamdvdr 0.1.0

Variable Density Reweighting for GaMD Simulations

GaMD Variable Density Reweighting (VDR)

Introduction

VDR is a python-based package for energetic reweighting of Gaussian Accelerated MD simulations. VDR provides a toolkit for calculating optimal boost parameters for GaMD simulations and performing post-hoc reweighting of GaMD simulation trajectories. VDR serves an improvement to the original PyReweighting script by Yinglong Miao (2014).

Installation

Using pip

pip install <UPDATE PYPI>

From source

git clone https://github.com/sct1g15/GaMD_Variable_Density_Reweighting.git
cd GaMD_Variable_Density_Reweighting
python setup.py install

Tutorial

This tutorial will take you through parameterisation and reweighting of a Gaussian Accelerated MD simulation.

Calculate the GaMD parameters

The VDR_param command calculates the highest standard deviation limits applicable to the amount of simulation frames you plan to save to your GaMD output trajectory. Default parameters assume a 0.01 anharmonicity tolerance, 0.02 kcal/mol standard error and 100 generated local clusters.

VDR_param --frames 950000

Run GaMD Simulation

Run your GaMD simulation, where the sum of the standard deviation limits used, should not exceed the value output by the VDR_param command.

Calculate CV values

Calculate the values of your CV of interest from the GaMD trajectory. This will vary between simulations, but an example script for calculating phi and psi angles from an alanine dipeptide example simulation have been provided in tutorial/phi_psi_calc.py. Formatting should match that in tutorial/data_example.dat, i.e. white spaced deliminated with three columns for CV1, CV2, frame number.

Combine Repeats (Optional)

VDR_comb supports multiple inputs if multiple repeats were used to concatenate results. This will output a data_concat.dat and gamd_concat.log file.

VDR_comb --data data1.dat data2.dat data3.dat data4.dat --gamd gamd1.log gamd2.log gamd3.log gamd4.log

Run VDR

Below is a minimum example for running VDR reweighting, this generate a single PMF distribution using a VDR cut-off of 9500:

VDR --gamd output/gamd.log --data input/data_example.txt --mode single --conv_points 9500 --pbc True --output output_VDR

For a more customised reweighting:

VDR --gamd output/gamd.log --data input/data_example.txt --cores 12 --emax 8 --mode convergence --conv_points 9500 --pbc True --output output_VDR

For details on all the arguments, you can use

VDR -h

References

Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA (2014) Improved reweighting of accelerated molecular dynamics simulations for free energy calculation. J Chemical Theory and Computation, 10(7): 2677-2689. Miao, Y., et al. (2015). Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. Journal of Chemical Theory and Computation 11(8): 3584-3595.