how to translate a protein without unfolding

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Wed Mar 27 2019 - 00:26:29 CDT

Dear all,

I have a system of two protein molecules (same type). I wand to move one
molecule while keeping the other molecule fixed and calculate the
interaction energy between the two molecules with relative position.

First, I added harmonic restraints to the backbone atoms of the molecule I
wanted to fix. Then I applied a constant force to all the atoms of the
other molecule and moved it in the direction I wanted.

However, I observed that, as the molecule moves, the protein starts to
unfold. I don't want this to happen. I want to only translate the molecule
without letting it unfold. If any of you can give some suggestions, that is
greatly appreciated.

Thank you.
Best regards,
Monika

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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