[gmx-users] which structure in NPT MD trjectory should be chosen to start another NVT MD?

[wuxiao]

Dear gmx users,

  Usually, we perform NPT MD to achieve optimized density of system and start another NVT MD to calculate other properties of interest.  I think there are three possible ways to choose the structure to start another NVT MD:(1) the structure of last step in NPT MD trjectory;(2)the structure in NPT MD trjectory with the density closest to the averaging density;(3)the structure of last step in NPT MD trjectory but the box size needs to be rescaled so that it is the averaging size. My question is: which way should be chosen to start another NVT MD? I do not know whether this question is suitable here. Any hints would be thanked very much.

Best wishes,

xiaowu

 

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