From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Tue Sep 01 2009 - 10:24:36 CDT
Please I would like to get some techniques-based comments on how people specify box dimensions for a melted lipid box.
I have a protein in a pre-equilibrated DPPC membrane with some lipid tails sticking sideways in the edges of the xy-plane. I am doing the following:
1. Measure minmax dimensions of the entire system in vmd.
2. Minimize sequentially the positions of hydrogen atoms, tail atoms, and all the atoms.
3. Heat the system from 0-310K at constant volume.
At the end of the heating my water box is distorted. Is this because the minmax including the tail groups sticking sideways resulted in a much larger box?
I tried using only the water molecules to get the minmax dimensions of the system. During the heating stage, the lipid leaflets separated and moved in opposite directions along the z-axis.
Please let me know how the minmax dimensions are typically obtained for a pre-equilibrated bilayer.
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