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
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)