Neural network based prediction of conformational free energies-a new route toward coarse-grained simulation models
Coarse-grained (CG) simulation models have become very popular tools to study complex
molecular systems with great computational efficiency on length and time scales that are …
molecular systems with great computational efficiency on length and time scales that are …
[HTML][HTML] Magic v. 3: An integrated software package for systematic structure-based coarse-graining
A Mirzoev, L Nordenskiöld, A Lyubartsev - Computer Physics …, 2019 - Elsevier
Molecular simulations of many phenomena related to biomolecular systems, soft matter and
nanomaterials require consideration of length scales above 10 nm and time scales longer …
nanomaterials require consideration of length scales above 10 nm and time scales longer …
Statistically optimal force aggregation for coarse-graining molecular dynamics
Machine-learned coarse-grained (CG) models have the potential for simulating large
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
A review of physics-based coarse-grained potentials for the simulations of protein structure and dynamics
By simplifying the atomistic representation of a biomolecular system, coarse-grained (CG)
approach enables the molecular dynamics simulation to reveal the biological processes …
approach enables the molecular dynamics simulation to reveal the biological processes …
A review of advancements in coarse-grained molecular dynamics simulations
SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …
large and complex systems in an efficient and inexpensive manner due to its lowered …
Multiconfigurational coarse-grained molecular dynamics
Standard low resolution coarse-grained modeling techniques have difficulty capturing
multiple configurations of protein systems. Here, we present a method for creating accurate …
multiple configurations of protein systems. Here, we present a method for creating accurate …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
[HTML][HTML] Multi-body effects in a coarse-grained protein force field
The use of coarse-grained (CG) models is a popular approach to study complex
biomolecular systems. By reducing the number of degrees of freedom, a CG model can …
biomolecular systems. By reducing the number of degrees of freedom, a CG model can …
Comment on “On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models” by M. Winger, D. Trzesniak, R. Baron …
SJ Marrink, X Periole, DP Tieleman… - Physical Chemistry …, 2010 - pubs.rsc.org
In a recent study published in this journal, Winger et al. 1 investigate the magnitude of the
time step to integrate the equations of motion in simulations with the coarse-grained …
time step to integrate the equations of motion in simulations with the coarse-grained …
Transferable and polarizable coarse grained model for proteins─ ProMPT
The application of classical molecular dynamics (MD) simulations at atomic resolution (fine-
grained level, FG), to most biomolecular processes, remains limited because of the …
grained level, FG), to most biomolecular processes, remains limited because of the …