Re: Membrane simulations

From: Elia Zumot (
Date: Tue Sep 01 2009 - 12:54:36 CDT

Hi Austin,

In general I wouldn't worry too much about the lipid tails pointing
outwards from the box. The .xst file will give you the dimensions upon
every step of the run.

If you have not yet equilibrated the system I suggest you use NPT and not
NVT since during equilibration the lipids would get closer to the protein
(I assume you have deleted the lipids within a certain diameter from the
protein right?) and water molecules will likely move more in between the
lipids and/or protein.

Since during equilibration the lipids should readjust around the protein
(and get closer) I suggest you solvate in slightly smaller dimensions than
the majority of lipids (bcz of the tails sticking out).

I usually try to keep at least 15A of lipids around the protein (x or y
directions) after equilibration.



> Hi everyone,
> 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.
> Thanks,
> Austin-

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