Provided by: gromacs-data_4.6.5-1build1_all bug


       g_membed - embeds a protein into a lipid bilayer

       VERSION 4.6.5


       g_membed   -f   into_mem.tpr  -n  index.ndx  -p  -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


        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.



       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

       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.


       -f into_mem.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input, Opt.
        Index file

       -p 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


        Print help info and quit

        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.

        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

        Call mdrun with membed options

        Be loud and noisy

       -mdrun_path string
        Path to the mdrun executable compiled with this g_membed version



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                              g_membed(1)