https://github.com/choderalab/saltswap
Package to fluctuate the number of counterions in an OpenMM simulation
Science Score: 23.0%
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Found 8 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (11.2%) to scientific vocabulary
Keywords
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Repository
Package to fluctuate the number of counterions in an OpenMM simulation
Basic Info
Statistics
- Stars: 6
- Watchers: 9
- Forks: 3
- Open Issues: 10
- Releases: 0
Topics
Metadata Files
README.md
saltswap
saltswap simulates dynamic anion-cation (salt) explicit solvent environments in OpenMM.
saltswap uses the semi-grand canonical ensemble to couple a simulation box to a reservoir at a given macroscopic salt concentration.
The applied chemical potential in saltswap reflects the salt concentration of the reservoir.
Citations
Please cite the following:
@article{saltswap,
author = {Gregory A. Ross, Ari\"{e}n S. Rustenburg, Patrick B. Grinaway, Josh Fass, and John D. Chodera.},
title = {Biomolecular simulations under realistic macroscopic salt conditions},
journal = {bioRxiv},
doi = {10.1101/226001}
year = {2017},
}
Installation
To install:
bash
python setup.py install
Dependencies are currently listed in saltswap/devtools/conda-recipe/meta.yaml.
Quick example
We'll first create a box water in which to try the insertion and deletion of salt:
python
from simtk import openmm, unit
from simtk.openmm import app
from openmmtools.testsystems import WaterBox
wbox = WaterBox(box_edge=25.0 * unit.angstrom, nonbondedMethod=app.PME,
cutoff=10 * unit.angstrom, ewaldErrorTolerance=1E-4)
Initializing the sampler that will perform Markov chain Monte Carlo by mixing
molecular dynamics moves that transform pairs of water molecules to anions and cations:
python
from saltswap.swapper import MCMCSampler
sampler = MCMCSampler(wbox.system, wbox.topology, wbox.positions, delta_chem=800)
The chemical potential is specified by delta_chem and is in kJ/mol.
The chemical potential corresponding to each macroscopic salt concentration must be calibrated for each water and ion pair forcefield, as well as the specific nonbonded treatment.
By default, saltswap makes instantaneous swaps between water and salt.
To achieve usable acceptance rates, we use nonequilibrium candidate Monte Carlo (NCMC).
To run a simulation for 1000 iterations of MD and salt-swap moves, we use the move method:
python
sampler.move(1000)
More detailed examples can be found in examples/.
Contributors
- Gregory Ross: gregory.ross@choderalab.org
- Bas Rustenburg: bas.rustenburg@choderalab.org
- John D. Chodera: john.chodera@choderalab.org
Owner
- Name: Chodera lab // Memorial Sloan Kettering Cancer Center
- Login: choderalab
- Kind: organization
- Email: john.chodera@choderalab.org
- Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY
- Website: http://choderalab.org
- Repositories: 269
- Profile: https://github.com/choderalab
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gregory Ross | g****k@g****m | 189 |
| gregoryross | G****s | 13 |
| John Chodera | j****a@c****g | 9 |
| John Chodera | c****j@m****g | 7 |
| Gregory A. Ross | g****k@G****m | 6 |
| Bas Rustenburg | b****g@c****g | 4 |
| Mike Henry | 1****y | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 2 years ago
All Time
- Total issues: 13
- Total pull requests: 18
- Average time to close issues: 16 days
- Average time to close pull requests: 2 days
- Total issue authors: 8
- Total pull request authors: 4
- Average comments per issue: 4.77
- Average comments per pull request: 1.0
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jchodera (5)
- gregoryross (2)
- matiasmachado (1)
- NelsonRamallo (1)
- davidlmobley (1)
- aghanbar (1)
- Mathsnel (1)
- bas-rustenburg (1)
Pull Request Authors
- gregoryross (13)
- jchodera (3)
- mikemhenry (1)
- bas-rustenburg (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- numpy *
- openmm *