g_membed Main Table of Contents

VERSION 4.6.3 Fri 5 Jul 2013

Description

g_membed embeds a membrane protein into an equilibrated lipid bilayer at the position and orientation specified by the user.

SHORT MANUAL
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The user should merge the structure files of the protein and membrane (+solvent), creating a single structure file with the protein overlapping the membrane at the desired position and orientation. The box size is taken from the membrane structure file. The corresponding topology files should also be merged. Consecutively, create a .tpr file (input for g_membed) from these files,with the following options included in the .mdp file.
- integrator = md
- energygrp = Protein (or other group that you want to insert)
- freezegrps = Protein
- freezedim = Y Y Y
- energygrp_excl = Protein Protein
The output is a structure file containing the protein embedded in the membrane. If a topology file is provided, the number of lipid and solvent molecules will be updated to match the new structure file.
For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.

SHORT METHOD DESCRIPTION
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1. The protein is resized around its center of mass by a factor -xy in the xy-plane (the membrane plane) and a factor -z in the z-direction (if the size of the protein in the z-direction is the same or smaller than the width of the membrane, a -z value larger than 1 can prevent that the protein will be enveloped by the lipids).
2. All lipid and solvent molecules overlapping with the resized protein are removed. All intraprotein interactions are turned off to prevent numerical issues for small values of -xy or -z
3. One md step is performed.
4. The resize factor (-xy or -z) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the protein is resized again around its center of mass. The resize factor for the xy-plane is incremented first. The resize factor for the z-direction is not changed until the -xy factor is 1 (thus after -nxy iterations).
5. Repeat step 3 and 4 until the protein reaches its original size (-nxy + -nz iterations).
For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.

NOTE
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- Protein can be any molecule you want to insert in the membrane.
- It is recommended to perform a short equilibration run after the embedding (see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly protein equilibration might require longer.

Files

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