MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation

Abstract

MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environment comprises the complete preparation-simulation–evaluation triad of a mesoscopic simulation task and especially enables biomolecular simulation tasks with peptides and proteins. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim allows for customized extensions for different fields of research.

MORTAR: a rich client application for in silico molecule fragmentation

“…This dates back to Bemis and Murcko’s investigation of the diversity of drug molecules known in their time by looking at how many different molecular frameworks can be identified and which of them appear very frequently [ 21 ]. A specific application of MORTAR could be the automated generation of adequate fragment molecule sets for mesoscopic simulation approaches of large molecular ensembles to be studied on the nanometer length and microsecond time scales (like “bottom-up” Dissipative Particle Dynamics (DPD) [ 54 ] supported by the MFsim/Jdpd [ 55 , 56 ] environment).…”

Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation

“…The need for volume scaling in concentration calculations is analyzed, with the conversion of the binary mixture composition to the specific volume-scaled molecular numbers of the simulation box described in Appendix 1 of [ 23 ]. For 18,500 C 10 E 4 molecules and a C 10 E 4 mass fraction of 0.75 this leads to 79,174 water molecules for C 10 E 4 fragmentation scheme A and 65,337 water molecules for scheme B.…”

Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics

“…All simulations are carried out with the open DPD environment MFsim [28,29], which utilizes the open Jdpd simulation kernel [3,30]. The sketched electrostatic interactions are implemented in Jdpd classes ParticlePairElectrostaticsDpdPotentialCalculator (for the potential energy between two charged particles) and ParticlePairElectrostaticsDpdForceCon-servativeCalculator (for the electrostatic forces of charged particles) in method calculateParti-clePairInteraction, in which the methods could be easily extended to alternative calculation schemes (e.g., [31]).…”