From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Thu Nov 18 2004 - 19:05:25 CST
I know that for most simulations using NAMD, one must minimize and equilibriate and then do a production run.
I wanted to confirm that when minimizing we are letting the protein come to a minimal energy state (sometimes PDB don't represent structures that are in a desirable state). When equilibrating the protein, we are letting the protein become "stable"??
Could someone comment on:
What the difference is between minimizing and equilibrating a protein?
Do we always have to equilibrate the protein before doing a production run?
How long should one minimize and equilibrate?
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