标题: 求助：做了一个500aa大小的二聚体蛋白模拟，200ns，审稿人提出rmsd未达到收敛 [打印本页] 作者Author: 胡枝子 时间: 2024-5-2 00:10 标题: 求助：做了一个500aa大小的二聚体蛋白模拟，200ns，审稿人提出rmsd未达到收敛 做了一个500aa大小的二聚体蛋白模拟，模拟时长200ns，审稿人提出rmsd未达到收敛。
问题1：Although each system deviates by 1 nm after 200 ns it does not mean the structures have stabilized or that the structures are similar. It would be true if the RMSD was small ~0.1 to 0.2 nm but 1 nm provides much scope for variation. This is always a challenge with large proteins.
问题2： To unambiguously interpret fluctuation data the simulations would need to be a) fully relaxed and then b) extensively sampled".
