SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation

• DOI: 10.1021/acs.jctc.7b01254
• Publication Date: 2018-03-06T01:04:44Z
• Authors: Jeremy D. Schmit; Nilusha L. Kariya...; Vince Needham; Paul E. Smith
• Keywords: Ions; 0301 basic medicine; 03 medical and health sciences; Static Electricity; Proteins; Molecular Dynamics Simulation; Sodium Chloride; Software

An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number ions simulation box to capture screening effects. However, that should be added is seldom given by bulk salt concentration because a charged biomolecule solute will perturb local solvent environment. We present simple method for calculating only total charge, volume, and as inputs. show most commonly used adding results an effective too high. These findings are confirmed using simulations lysozyme. have established web server where these calculations can readily performed aid setup.