[gmx-users] reproducibility of trajectory

Qing Lv lvqingjiejie at 163.com
Wed Aug 19 10:30:49 CEST 2015


I did a 200-ns MD for a protein and found an interesting conformation transition, and according to NMR study in literature, it is believed that 10 us ~ ms scale simulations are needed to get this conformation transition.
However, when I tried to reproduce this conformation transition, I was not so lucky any more... I repeated 6 x 200ns trajectories but failed to reproduce, even I used the same seed number.
Do you have any ideas on this? Is it sufficient to present this result in papers, since I just got 1 trajectory?


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