V. Gapsys

Periodic boundaries in Molecular Dynamics simulations: why do we need salt?

This paper investigates how periodic boundary conditions in MD simulations affect systems with uncompensated dipoles, showing that ions help mitigate unwanted artifacts caused by these dipoles.

Comment on ‘Response to comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’’

The paper challenges the conclusions of a previous study on box size effects in hemoglobin MD simulations, identifies additional flaws in the response, and reasserts concerns about the validity of the original claims.

Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase

The paper uses molecular dynamics simulations to study phospholipid transport and specificity in a flippase, revealing a preference for phosphatidylserine and insights into substrate selectivity mechanisms.

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

This study evaluates binding free energy calculation methods using the SAMPL6 challenge, finding variations in efficiency and reproducibility across different systems and methods.

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

The paper critiques a study on hemoglobin stability in molecular dynamics simulations, arguing that its findings on box size dependence are not reproducible with more statistics.