[AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016

From: Akshay Prabhakant <akshayresearch16.gmail.com>
Date: Mon, 13 May 2019 19:23:49 +0530

Hello everyone,

I am trying to vary the distance between 2 alpha helices, and have set up
my distance restraints to study that. However, for certain distances, the
helices get really stretched out and lose most of their helicity. I then
set up additional distance restraints to constrain the length of the
helices to their initial value, but that resulted in similar weird
stretching out/bending of the helix.

Using COM distance based restraints, how do I keep my alpha helices from
losing their shape? I would like to treat both helices as rigid bodies
during the course of my simulation.

Thank you,

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Received on Mon May 13 2019 - 07:00:03 PDT
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