https://github.com/konermannlab/esi_droplet_na_bradykinin
MD simulation of an evaporating ESI droplet, with TIP4P/2005 water, Na ions, and bradykinin (peptide)
https://github.com/konermannlab/esi_droplet_na_bradykinin
charged droplet electrospray evaporation ion md model peptide protein residue simulation
Last synced: about 1 month ago
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MD simulation of an evaporating ESI droplet, with TIP4P/2005 water, Na ions, and bradykinin (peptide)
- Host: GitHub
- URL: https://github.com/konermannlab/esi_droplet_na_bradykinin
- Owner: KonermannLab
- License: unlicense
- Created: 2025-07-15T17:58:35.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2025-07-15T18:00:51.000Z (4 months ago)
- Last Synced: 2025-09-11T16:49:40.018Z (about 2 months ago)
- Topics: charged, droplet, electrospray, evaporation, ion, md, model, peptide, protein, residue, simulation
- Homepage:
- Size: 781 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ESI_droplet_NA_bradykinin
MD simulation of an evaporating ESI droplet, with TIP4P/2005 water, Na ions, and bradykinin (peptide)
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ESI DROPLET SIMULATION PACKAGE (provided by Lars Konermann, The University of Western Ontario)
This package contains two directories that allow simulations of evaporating ESI droplets that contain a peptide (or protein).
To execute the files, run the bash scripts in each directory.
The droplets consist of TIP4P/2005 water, with Na+ ions, and with a peptide ion (here: bradykinin3+).
The package was tested with Gromacs 2020.4, but other Gromacs versions will likely be ok.
/Simple
contains a pre-assembled droplet that is about to undergo peptide IEM ejection.
You should try this first, to test for bugs etc.
/Complete
generates a droplet from scratch, performs multiple rounds of trajectory stitching (evaporation), culminating in peptide CRM.
By modifying input parameters, these files allow simulations on a wide range of droplet systems.
For setting up new peptide (or protein) gro and itp starting files, use pdb2gmx.
Questions?
Lars Konermann
konerman@uwo.ca
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When using these files, please cite:
"MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation" K. Hanifi, P. M. Scrosati, and L. Konermann J. Phys. Chem. B 128, 5973-5986 (2024).
https://pubs.acs.org/doi/10.1021/acs.jpcb.4c01241
(mdp files included in the current package reflect the H2*(g) settings of this paper)