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

[Mark Abraham]

wuxiao wrote:
> 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.

Bear in mind in your averaging that you're actually interested in the
average *after* equilibration, which often does not include the start of
a trajectory.

Otherwise, I think it's largely irrelevant except that you don't want a
density that's noticeably different from the one used in
parameterization of the forcefield. You'll still need a period of
further equilibration after any of the above choices.

Mark