how to translate a protein without unfolding

From: Monika Madhavi (
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,

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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:40 CST