AMBER Archive (2006)

Subject: AMBER: MM-PBSA

From: Shozeb Haider (shozeb.haider_at_pharmacy.ac.uk)
Date: Mon Dec 18 2006 - 11:57:17 CST

Hi

I am trying to perform MM-PBSA calculations on an MD run (10ns). I have
been reading several protocols and I was wondering about 2 things.

1. How would my calculations differ if I take snapshots every 250ps over
the last 8ns instead of snapshots taken at 10ps interval during the last
2ns of my simulations ?

2. Why is latter the preferred method ?

I shall extremely grateful to make me understand this point.

Best wishes

Shozeb Haider
The London School of Pharmacy
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