A canonical replica exchange molecular dynamics implementation with normal pressure in each replica

Area of Science:

• Computational chemistry
• Molecular dynamics simulations
• Statistical mechanics

Background:

• Conventional constant NPT-REMD is difficult for some systems.
• Constant NVT-REMD can introduce pressure artifacts at elevated temperatures.
• Accurate simulation of systems with complex interfaces or constraints is challenging.

Purpose of the Study:

• To present a novel replica exchange molecular dynamics (REMD) simulation method, REMD-NV(p)T, suitable for systems where conventional NPT setups are difficult.
• To validate the accuracy of REMD-NV(p)T against established simulation ensembles.
• To assess the impact of pressure and barostats on molecular dynamics.

Main Methods:

• Development of a new canonical replica exchange molecular dynamics (REMD) simulation method with normal pressure for all replicas (REMD-NV(p)T).
• Derivation of a novel exchange term for the REMD-NV(p)T method.
• Validation using structural properties of SPC/E water and dialanine (Ala2) in bulk and near a graphene layer.

Main Results:

• REMD-NV(p)T shows good agreement with NPT-ensemble simulations for structural properties across all temperatures.
• The new method corrects for high-pressure artifacts observed in constant NVT-ensemble simulations at elevated temperatures.
• Dynamical eigenmodes from REMD-NV(p)T closely match NVT-ensemble results, unlike NPT implementations.

Conclusions:

• The REMD-NV(p)T method provides an accurate and robust alternative for molecular dynamics simulations where conventional NPT is challenging.
• This method effectively captures structural properties without introducing artifacts from barostat presence.
• REMD-NV(p)T offers a valuable tool for studying complex molecular systems, preserving essential dynamical characteristics.