【摘要】 使用ff12SB力场和广义玻恩(GB-Neck2)隐性水模型在GTX670 GPU上对4个蛋白质CLN025(2ZEI)、MHA6(2I9M)、Trp-Cage(1L2Y)、Villin(3TRW)的微秒级折叠过程进行了分子动力学模拟,2ZEI的折叠时间和均方根偏差为5.94μs和0.897,2I9M的折叠时间和均方根偏差为0.191μs和1.142,Villin的折叠时间和均方根偏差为4.23μs和1.37,Trp-Cage的折叠时间和均方根偏差为2.48μs和0.63。结果表明,蛋白质折叠模拟已经能够通过GPU计算在桌面计算机上实现。更多还原

【Abstract】 We performed molecular dynamics simulation for four proteins,CLN025( 2ZEI),MHA6( 2I9M),Trp-Cage( 1L2Y) and Villin( 3TRW) on GEX670-GPU with AMBER ff12 SB force field and Generalized Born( GB-Neck2) implicit solvent model. Results show that folding time and RMSD compared to its crystal structure are 5. 94 μs and 0. 897  for protein 2ZEI,0. 191 μs and 1.142 for protein 219 M,4. 23 μs and 1. 37  for protein Villin,and 2. 49 μs and 0. 63  protein Trp-Cage. It demonstrates that microsecond level protein folding simulation can be implemented on a desktop workstation with GPU computing.更多还原