[gmx-users] Does One need to set comm_mode = none for an equilibrium MD to get exact MSD?

[Hu Zhongqiao]

Dear all,

 

When I run equilibrium MD simulation, I did not do anything for COM
removal in .mdp file. So by default, the linear motion of COM of the
whole system should be removed. In this case, the MSD calculated by
g_msd should be different from that otherwise. So one needs to set
comm_mode = none?

 

Thanks,

Zhongqiao

 

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