SYNOPSIS
g_membed -f into_mem.tpr -n index.ndx -p topol.top -o traj.trr -x traj.xtc -cpi state.cpt -cpo state.cpt -c membedded.gro -e ener.edr -g md.log -ei sam.edi -rerun rerun.xtc -table table.xvg -tablep tablep.xvg -tableb table.xvg -dhdl dhdl.xvg -field field.xvg -table table.xvg -tablep tablep.xvg -tableb table.xvg -rerun rerun.xtc -tpi tpi.xvg -tpid tpidist.xvg -ei sam.edi -eo sam.edo -j wham.gct -jo bam.gct -ffout gct.xvg -devout deviatie.xvg -runav runaver.xvg -px pullx.xvg -pf pullf.xvg -mtx nm.mtx -dn dipole.ndx -multidir rundir -[no]h -[no]version -nice int -deffnm string -xvg enum -xyinit real -xyend real -zinit real -zend real -nxy int -nz int -rad real -pieces int -[no]asymmetry -ndiff int -maxwarn int -[no]compact -[no]vDESCRIPTION
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
- 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
------------------------
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 InputRun 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)
-cpi state.cpt
Input, Opt.
Checkpoint file
-cpo state.cpt
Output, Opt.
Checkpoint file
-c membedded.gro
Output
Structure file: gro g96 pdb etc.
-e ener.edr
Output
Energy file
-g md.log
Output
Log file
-ei sam.edi
Input, Opt.
ED sampling input
-rerun rerun.xtc
Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-table table.xvg
Input, Opt.
xvgr/xmgr file
-tablep tablep.xvg
Input, Opt.
xvgr/xmgr file
-tableb table.xvg
Input, Opt.
xvgr/xmgr file
-dhdl dhdl.xvg
Output, Opt.
xvgr/xmgr file
-field field.xvg
Output, Opt.
xvgr/xmgr file
-table table.xvg
Input, Opt.
xvgr/xmgr file
-tablep tablep.xvg
Input, Opt.
xvgr/xmgr file
-tableb table.xvg
Input, Opt.
xvgr/xmgr file
-rerun rerun.xtc
Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg
Output, Opt.
xvgr/xmgr file
-tpid tpidist.xvg
Output, Opt.
xvgr/xmgr file
-ei sam.edi
Input, Opt.
ED sampling input
-eo sam.edo
Output, Opt.
ED sampling output
-j wham.gct
Input, Opt.
General coupling stuff
-jo bam.gct
Output, Opt.
General coupling stuff
-ffout gct.xvg
Output, Opt.
xvgr/xmgr file
-devout deviatie.xvg
Output, Opt.
xvgr/xmgr file
-runav runaver.xvg
Output, Opt.
xvgr/xmgr file
-px pullx.xvg
Output, Opt.
xvgr/xmgr file
-pf pullf.xvg
Output, Opt.
xvgr/xmgr file
-mtx nm.mtx
Output, Opt.
Hessian matrix
-dn dipole.ndx
Output, Opt.
Index file
-multidir rundir
Input, Opt., Mult.
Run directory
OTHER OPTIONS
-[no]hnoPrint help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-deffnm string
Set the default filename for all file options
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-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]compactyes
Write a compact log file
-[no]vno
Be loud and noisy