Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_membed - embeds a protein into a lipid bilayer
VERSION 4.6.5
SYNOPSIS
g_membed -f into_mem.tpr -n index.ndx -p topol.top -o traj.trr -x traj.xtc -c membedded.gro -e ener.edr
-dat membed.dat -[no]h -[no]version -nice int -xyinit real -xyend real -zinit real -zend real -nxy int
-nz int -rad real -pieces int -[no]asymmetry -ndiff int -maxwarn int -[no]start -[no]v -mdrun_path string
DESCRIPTION
g_membed embeds a membrane protein into an equilibrated lipid bilayer at the position and orientation
specified by the user.
SHORT MANUAL ------------
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
- energygrps = 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
------------------------
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 ----
- 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
-f into_mem.tpr Input
Run input file: tpr tpb tpa
-n index.ndx Input, Opt.
Index file
-p topol.top In/Out, Opt.
Topology file
-o traj.trr Output
Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt.
Compressed trajectory (portable xdr format)
-c membedded.gro Output
Structure file: gro g96 pdb etc.
-e ener.edr Output
Energy file
-dat membed.dat Output
Generic data file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-xyinit real 0.5
Resize factor for the protein in the xy dimension before starting embedding
-xyend real 1
Final resize factor in the xy dimension
-zinit real 1
Resize factor for the protein in the z dimension before starting embedding
-zend real 1
Final resize faction in the z dimension
-nxy int 1000
Number of iteration for the xy dimension
-nz int 0
Number of iterations for the z dimension
-rad real 0.22
Probe radius to check for overlap between the group to embed and the membrane
-pieces int 1
Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own
geometrical center.
-[no]asymmetryno
Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not
be checked.
-ndiff int 0
Number of lipids that will additionally be removed from the lower (negative number) or upper (positive
number) membrane leaflet.
-maxwarn int 0
Maximum number of warning allowed
-[no]startno
Call mdrun with membed options
-[no]vno
Be loud and noisy
-mdrun_path string
Path to the mdrun executable compiled with this g_membed version
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 2 Dec 2013 g_membed(1)