We continue adding new features onto sDMD and keep improving the performance.
Comparing with the old version v0.95, the new version includes, but not limited, the following major modifications:
- bugs fixed.
- temporarily removed the multi-thread code and focused on single-thread performance improvement.
- added a CG model (Go-like model) for the interactions between protein/peptide and different types of surfaces (hydrophobic, hydrophilic, relative-hydrophobic) based on the paper of Shuai Wei and Thomas A. Knotts IV (JCP, 2013).
- made REMD simulation easier.
Please note that, during the optimizations, we may have modified the data structures, configuration file, breakpoint file, etc., thus the older files may not be able to be run on the new version.
Some details in the manual/readme/paper (Size Zheng, Computer Physics Communications, 2020) would be outdated. We will try our best to follow up in a timely manner.
Please stay safe and stay healthy!