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Updated: Jul 1, 2026
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
Published on: April 12, 2019
CondenSimAdapter: A Versatile Builder for Multiscale Simulations of Protein Condensates with Broad Force-Field
Xiaojing Tian1,2, Wei Han3,4,2
1School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
Journal of Chemical Information and Modeling
|June 30, 2026
Summary
CondenSimAdapter resolves the challenge of converting coarse-grained to all-atom models for biomolecular simulations. This Python package overcomes steric clashes, enabling efficient and accurate studies of protein phase separation.
Area of Science:
- Computational Biology
- Biophysics
- Molecular Dynamics
Background:
- Multiscale molecular dynamics simulations are crucial for studying biomolecular condensates.
- Building all-atom (AA) systems from coarse-grained (CG) models presents a "relaxation bottleneck" due to steric clashes.
Purpose of the Study:
- Introduce CondenSimAdapter, a Python package to bridge the resolution gap between CG and AA simulations.
- Facilitate efficient backmapping and relaxation of dense condensate configurations.
Main Methods:
- Integrate SE(3)-transformer-based cg2all backmapping with a novel physics-inspired optimization protocol.
- Utilize Gaussian repulsion and soft-core potentials to resolve steric clashes.
- Unify four CG and nine AA force fields within a single interface.
Main Results:
- Successfully eliminated major structure conflicts across diverse CG-AA combinations.
- Preserved structural integrity of multidomain proteins.
- Validated ensemble fidelity with a 2 μs all-atom simulation of FUS LC condensate, reproducing key properties.
Conclusions:
- CondenSimAdapter effectively resolves the dense-phase relaxation bottleneck in multiscale simulations.
- Lowers the technical barrier for studying protein phase separation.
- Enables systematic, high-throughput investigations of biomolecular condensates.
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