Tools to "open" domains

From: ARTURAS ZIEMYS (ziemys.1_at_osu.edu)
Date: Tue Jan 31 2006 - 10:12:03 CST

HI,

My protein has two domains and I want to "open" then using NAMD.
Can anybody give me advice or tips to do that ?

Can any assign two centers of masses for each domain and apply some force to "open" domains ?

I am not sure about what is the best to choose from NAMD tools (define harmonic constrains between the center of masses for both domains? To use SMD or ABF ?)

Any advices welcome
With best
Arturas Z.

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