impose restraint on the internal coordinate of protein

From: dhacademic (dhacademic_at_gmail.com)
Date: Mon Jun 21 2010 - 13:43:58 CDT

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Hi, I have a question about imposing restraint on protein.

In my system, a dimer-of-dimer structure (protein) is merged in a water box, say dimer A (with monomer a and b) and dimer A' (with monomer a' and b'). I want to keep the structures as well as the relative orientation within the dimer, but to search the optimal orientation between the two dimers by MD simulations. How can I impose this kind of restraint in NAMD?

Thanks in advance.

Hao Dong

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