From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Nov 22 2013 - 10:49:17 CST
----- Original Message -----
> Thanks for the reply Jerome.
> Now, for each window I have 5000 minimization followed by 10000 steps. I
> did try going to 10^6 steps, but didn't give significant difference in free
> energy.
In general I wouldn't recommend minimizing between windows. You have to thermalize to room temperature again every time, and discard the additional equilibration time.
> So just to be clear, in the previous message by saying "increase the
> sampling time for just those two by running extra simulations" you meant
> going to smaller dlambda values between 0.45 and 0.55?
I meant running more MD for the same lambda and dlambda values.
> Also, does it make sense to do FEP just between 0.45 and 0.55 and then use
> it with data for all other windows?
Yes, you can merge any amount of data from separate runs. How to do it properly depends on what free energy estimator you use. For the FEP estimator, it's just a matter of taking the log of a weighted average of exponenials of deltaGs.
Jerome
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