.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_membed - embeds a protein into a lipid bilayer .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_membed\fP .BI "\-f" " into_mem.tpr " .BI "\-n" " index.ndx " .BI "\-p" " topol.top " .BI "\-o" " traj.trr " .BI "\-x" " traj.xtc " .BI "\-cpi" " state.cpt " .BI "\-cpo" " state.cpt " .BI "\-c" " membedded.gro " .BI "\-e" " ener.edr " .BI "\-g" " md.log " .BI "\-ei" " sam.edi " .BI "\-rerun" " rerun.xtc " .BI "\-table" " table.xvg " .BI "\-tablep" " tablep.xvg " .BI "\-tableb" " table.xvg " .BI "\-dhdl" " dhdl.xvg " .BI "\-field" " field.xvg " .BI "\-table" " table.xvg " .BI "\-tablep" " tablep.xvg " .BI "\-tableb" " table.xvg " .BI "\-rerun" " rerun.xtc " .BI "\-tpi" " tpi.xvg " .BI "\-tpid" " tpidist.xvg " .BI "\-ei" " sam.edi " .BI "\-eo" " sam.edo " .BI "\-j" " wham.gct " .BI "\-jo" " bam.gct " .BI "\-ffout" " gct.xvg " .BI "\-devout" " deviatie.xvg " .BI "\-runav" " runaver.xvg " .BI "\-px" " pullx.xvg " .BI "\-pf" " pullf.xvg " .BI "\-mtx" " nm.mtx " .BI "\-dn" " dipole.ndx " .BI "\-multidir" " rundir " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-deffnm" " string " .BI "\-xvg" " enum " .BI "\-xyinit" " real " .BI "\-xyend" " real " .BI "\-zinit" " real " .BI "\-zend" " real " .BI "\-nxy" " int " .BI "\-nz" " int " .BI "\-rad" " real " .BI "\-pieces" " int " .BI "\-[no]asymmetry" "" .BI "\-ndiff" " int " .BI "\-maxwarn" " int " .BI "\-[no]compact" "" .BI "\-[no]v" "" .SH DESCRIPTION \&\fB g_membed\fR 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 \fB .tpr\fR file (input for \fB g_membed\fR) from these files,with the following options included in the \fB .mdp\fR file. \& \- \fB integrator = md\fR \& \- \fB energygrp = Protein\fR (or other group that you want to insert) \& \- \fB freezegrps = Protein\fR \& \- \fB freezedim = Y Y Y\fR \& \- \fB energygrp_excl = Protein Protein\fR \&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 \fB \-xy\fR in the xy\-plane \&(the membrane plane) and a factor \fB \-z\fR in the \fI z\fR\-direction (if the size of the \&protein in the z\-direction is the same or smaller than the width of the membrane, a \&\fB \-z\fR 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 \fB \-xy\fR \& or \fB \-z\fR \&3. One md step is performed. \&4. The resize factor (\fB \-xy\fR or \fB \-z\fR) 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 \fB \-xy\fR factor \&is 1 (thus after \fB \-nxy\fR iterations). \&5. Repeat step 3 and 4 until the protein reaches its original size (\fB \-nxy\fR + \fB \-nz\fR 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. .SH FILES .BI "\-f" " into_mem.tpr" .B Input Run input file: tpr tpb tpa .BI "\-n" " index.ndx" .B Input, Opt. Index file .BI "\-p" " topol.top" .B In/Out, Opt. Topology file .BI "\-o" " traj.trr" .B Output Full precision trajectory: trr trj cpt .BI "\-x" " traj.xtc" .B Output, Opt. Compressed trajectory (portable xdr format) .BI "\-cpi" " state.cpt" .B Input, Opt. Checkpoint file .BI "\-cpo" " state.cpt" .B Output, Opt. Checkpoint file .BI "\-c" " membedded.gro" .B Output Structure file: gro g96 pdb etc. .BI "\-e" " ener.edr" .B Output Energy file .BI "\-g" " md.log" .B Output Log file .BI "\-ei" " sam.edi" .B Input, Opt. ED sampling input .BI "\-rerun" " rerun.xtc" .B Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-table" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tablep" " tablep.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tableb" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-dhdl" " dhdl.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-field" " field.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-table" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tablep" " tablep.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tableb" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-rerun" " rerun.xtc" .B Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-tpi" " tpi.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-tpid" " tpidist.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ei" " sam.edi" .B Input, Opt. ED sampling input .BI "\-eo" " sam.edo" .B Output, Opt. ED sampling output .BI "\-j" " wham.gct" .B Input, Opt. General coupling stuff .BI "\-jo" " bam.gct" .B Output, Opt. General coupling stuff .BI "\-ffout" " gct.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-devout" " deviatie.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-runav" " runaver.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-px" " pullx.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-pf" " pullf.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-mtx" " nm.mtx" .B Output, Opt. Hessian matrix .BI "\-dn" " dipole.ndx" .B Output, Opt. Index file .BI "\-multidir" " rundir" .B Input, Opt., Mult. Run directory .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-deffnm" " string" " " Set the default filename for all file options .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-xyinit" " real" " 0.5 " Resize factor for the protein in the xy dimension before starting embedding .BI "\-xyend" " real" " 1 " Final resize factor in the xy dimension .BI "\-zinit" " real" " 1 " Resize factor for the protein in the z dimension before starting embedding .BI "\-zend" " real" " 1 " Final resize faction in the z dimension .BI "\-nxy" " int" " 1000" Number of iteration for the xy dimension .BI "\-nz" " int" " 0" Number of iterations for the z dimension .BI "\-rad" " real" " 0.22 " Probe radius to check for overlap between the group to embed and the membrane .BI "\-pieces" " int" " 1" Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center. .BI "\-[no]asymmetry" "no " Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked. .BI "\-ndiff" " int" " 0" Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet. .BI "\-maxwarn" " int" " 0" Maximum number of warning allowed .BI "\-[no]compact" "yes " Write a compact log file .BI "\-[no]v" "no " Be loud and noisy .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.