[gmx-users] Is minimization and equilibration needed for umbrella sampling?

[Justin Lemkul]

On 1/10/20 11:02 AM, Qing Lv wrote:
> Dear Colleagues,
>
>
> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was closed to the center of the window. So, need I do energy-minimization and equilibration for each window? Since each initial conformation has no bad clashes (actually they can run MD well without minimizations) and is closed to the window center, I cannot understand why minimization and equilibration are still needed (as a lot of references do so).

I don't think minimization is essential, but unless you saved the full 
state (including velocities) for each snapshot, then you need to 
re-equilibrate. Otherwise you're either starting from T=0 K (gen-vel=no) 
or a random state that is not necessarily stable (gen-vel=yes).

-Justin

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Justin A. Lemkul, Ph.D.
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