Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
The AA trajectories are modified by manual processing
此次修改仅添加了粗粒化轨迹的被优化分子居中处理，而优化用到的全原子轨迹需要自己提前手动做相应处理。
I thank Charly Empereur-Mot, Luca Pesce, Giovanni Doni, Davide Bochicchio, Riccardo Capelli, Claudio Perego, and Giovanni M. Pavan for their valuable works
References：
Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization.
Charly Empereur-Mot, Luca Pesce, Giovanni Doni, Davide Bochicchio, Riccardo Capelli, Claudio Perego, and Giovanni M. Pavan.
ACS Omega 2020 5 (50), 32823-32843
DOI: 10.1021/acsomega.0c05469
This branch has the following changes
The following error message is fixed:TypeError: center() got an unexpected keyword argument 'pbc'
修复Mdanalysis的center函数变更引起的报错：TypeError: center() got an unexpected keyword argument 'pbc'
Added periodic processing(gmx_cmd = f'echo 2 0 | {ns.gmx_path} trjconv -s md.tpr -f md.xtc -pbc mol -center -o md.xtc') of coarse-grained simulation tracks
添加了优化过程中每步产生的粗粒化轨迹的周期性处理：将被优化分子的轨迹周期性处理并且居中，消除分子裂开的情况（也就是所谓的jump或者wrap的情况）。
Note
The AA trajectories are modified by manual processing
此次修改仅添加了粗粒化轨迹的被优化分子居中处理，而优化用到的全原子轨迹需要自己提前手动做相应处理。
I thank Charly Empereur-Mot, Luca Pesce, Giovanni Doni, Davide Bochicchio, Riccardo Capelli, Claudio Perego, and Giovanni M. Pavan for their valuable works
References： Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. Charly Empereur-Mot, Luca Pesce, Giovanni Doni, Davide Bochicchio, Riccardo Capelli, Claudio Perego, and Giovanni M. Pavan. ACS Omega 2020 5 (50), 32823-32843 DOI: 10.1021/acsomega.0c05469
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