**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Fri Nov 22 2013 - 10:49:17 CST

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----- Original Message -----

*> Thanks for the reply Jerome.
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*> Now, for each window I have 5000 minimization followed by 10000 steps. I
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*> did try going to 10^6 steps, but didn't give significant difference in free
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*> energy.
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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
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*> sampling time for just those two by running extra simulations" you meant
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*> going to smaller dlambda values between 0.45 and 0.55?
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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
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*> it with data for all other windows?
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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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