Trajectory data of molecular dynamics simulation of SARS-CoV-2 Main Protease and inhibitor drug candidates

MD simulations were performed using Desmond on supercomputer TSUBAME 3.0. The inhibitor-SARS-CoV-2 Mpro complex models were placed in the orthorhombic box with a buffer distance of 10 Å in order to create a hydration model. TIP3P water model was used for creation of the hydration model. We performed MD simulations under the NPT ensemble for 1 μs on three complex structures using OPLS3e force field.本研究采用Desmond软件，于超级计算机TSUBAME 3.0上开展分子动力学（Molecular Dynamics, MD）模拟。将抑制剂-严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）主蛋白酶（Mpro）复合物模型置于正交晶胞盒子中，设置10埃的缓冲距离以构建水合模型，该水合模型采用TIP3P水模型进行构建。针对3种复合物结构，本研究使用OPLS3e力场，在NPT系综下开展了时长为1微秒的分子动力学模拟。