PyCGTOOL: automated generation of coarse-grained molecular dynamics models from atomistic trajectories
Development of coarse-grained (CG) molecular dynamics models is often a laborious
process which commonly relies upon approximations to similar models, rather than …
process which commonly relies upon approximations to similar models, rather than …
OpenMSCG: A software tool for bottom-up coarse-graining
The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …
computational models to simulate large-scale and complex phenomena and processes, is …
[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 …
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 …
Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS
V Niranjan, P Rao, A Uttarkar, J Kumar - Plos one, 2023 - journals.plos.org
Coarse-grained simulations have emerged as a valuable tool in the study of large and
complex biomolecular systems. These simulations, which use simplified models to represent …
complex biomolecular systems. These simulations, which use simplified models to represent …
SIRAH tools: mapping, backmapping and visualization of coarse-grained models
MR Machado, S Pantano - Bioinformatics, 2016 - academic.oup.com
Coarse-grained (CG) models reduce the cost of molecular dynamics simulations keeping
the essence of molecular interactions. Still, the diversity of CG representations (sizes …
the essence of molecular interactions. Still, the diversity of CG representations (sizes …
K-Means Clustering Coarse-Graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-Grained Mappings of Large Biomolecules
Coarse-grained (CG) molecular dynamics (MD) has become a method of choice for
simulating various large scale biomolecular processes; therefore, the systematic definition of …
simulating various large scale biomolecular processes; therefore, the systematic definition of …
Backmapping from multiresolution coarse-grained models to atomic structures of large biomolecules by restrained molecular dynamics simulations using bayesian …
Coarse-grained (CG) simulations have allowed access to larger length scales and longer
time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) …
time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) …
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 …