Only part of the protein is moving in MD simulation

From: Uma Mahankali (
Date: Wed Oct 26 2005 - 10:12:13 CDT


I am running a simulation of a membrane protein in water box with PBC and I
imposed a harmonic constraint of 0.5 kcal/mol on the protein atoms. Even
after 1 ns of equilibration, only the bottom part of the protein has moved a
bit and the top part has not moved at all. I am suspecting that it could be
because of high pressure (I am running an NVT simulation).

Has anyone observed such a trend before?


Uma Mahankali,
Graduate Student,
Department of Chemistry,
University of Cincinnati,

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