g_membed(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_membed(1)

NAME

       g_membed - embeds a protein into a lipid bilayer

       VERSION 4.5.4-dev-20110404-bc5695c

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]v

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  over-
       lapping	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-direc-
       tion  (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  pre-
       vent 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)

       -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]hno
	Print 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

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_membed(1)