From: doty alexiou (
Date: Thu Dec 03 2009 - 15:06:49 CST

Hello. I want to ask what kind of constraints should i use in order to keep the tertiary structure of a protein in a cg simulation. I guess i should not restain atoms on certain coordinates or on a certain direction, but i should constrain the distance between pairs of atoms. So, harmonic bonds through steered molecular dynamics would be the right feature of NAMD?Thank you.


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