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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_membed</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 g_membed embeds a membrane protein into an equilibrated lipid bilayer at the position
  18 and orientation specified by the user.
  19
  20
  21
  22 SHORT MANUAL
  23 ------------
  24
  25 The user should merge the structure files of the protein and membrane (+solvent), creating a
  26 single structure file with the protein overlapping the membrane at the desired position and
  27 orientation. Box size should be taken from the membrane structure file. The corresponding topology
  28 files should also be merged. Consecutively, create a <a href="tpr.html">tpr</a> file (input for g_membed) from these files,with the following options included in the <a href="mdp.html">mdp</a> file.
  29
  30  - integrator      = md
  31
  32  - energygrp       = Protein (or other group that you want to insert)
  33
  34  - freezegrps      = Protein
  35
  36  - freezedim       = Y Y Y
  37
  38  - energygrp_excl  = Protein Protein
  39
  40 The output is a structure file containing the protein embedded in the membrane. If a topology
  41 file is provided, the number of lipid and
  42 solvent molecules will be updated to match the new structure file.
  43
  44 For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.
  45
  46
  47
  48 SHORT METHOD DESCRIPTION
  49
  50 ------------------------
  51
  52 1. The protein is resized around its center of mass by a factor -xy in the xy-plane
  53 (the membrane plane) and a factor -z in the z-direction (if the size of the
  54 protein in the z-direction is the same or smaller than the width of the membrane, a
  55 -z value larger than 1 can prevent that the protein will be enveloped by the lipids).
  56
  57 2. All lipid and solvent molecules overlapping with the resized protein are removed. All
  58 intraprotein interactions are turned off to prevent numerical issues for small values of -xy
  59  or -z
  60
  61 3. One md step is performed.
  62
  63 4. The resize factor (-xy or -z) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the
  64 protein is resized again around its center of mass. The resize factor for the xy-plane
  65 is incremented first. The resize factor for the z-direction is not changed until the -xy factor
  66 is 1 (thus after -nxy iteration).
  67
  68 5. Repeat step 3 and 4 until the protein reaches its original size (-nxy + -nz iterations).
  69
  70 For a more extensive method descrition see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.
  71
  72
  73
  74 NOTE
  75 ----
  76
  77  - Protein can be any molecule you want to insert in the membrane.
  78
  79  - It is recommended to perform a short equilibration run after the embedding
  80 (see Wolf et al, J Comp Chem 31 (2010) 2169-2174, to re-equilibrate the membrane. Clearly
  81 protein equilibration might require longer.
  82
  83
  84
  85 <P>
  86 <H3>Files</H3>
  87 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  88 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">into_mem.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">   topol.top</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Topology file </TD></TR>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html">    traj.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-cpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html">   state.cpt</a></tt> </TD><TD> Input, Opt. </TD><TD> Checkpoint file </TD></TR>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-cpo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html">   state.cpt</a></tt> </TD><TD> Output, Opt. </TD><TD> Checkpoint file </TD></TR>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">membedded.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  97 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Output </TD><TD> Energy file </TD></TR>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">      md.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html">     sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-dhdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-field</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   field.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
 110 <TR><TD ALIGN=RIGHT> <b><tt>-tpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     tpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 111 <TR><TD ALIGN=RIGHT> <b><tt>-tpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpidist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 112 <TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html">     sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
 113 <TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html">     sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
 114 <TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">    wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
 115 <TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">     bam.gct</a></tt> </TD><TD> Output, Opt. </TD><TD> General coupling stuff </TD></TR>
 116 <TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 117 <TR><TD ALIGN=RIGHT> <b><tt>-devout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">deviatie.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 118 <TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 119 <TR><TD ALIGN=RIGHT> <b><tt>-px</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   pullx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 120 <TR><TD ALIGN=RIGHT> <b><tt>-pf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   pullf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 121 <TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html">      nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
 122 <TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">  dipole.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
 123 </TABLE>
 124 <P>
 125 <H3>Other options</H3>
 126 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 127 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 128 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
 129 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
 130 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
 131 <TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options </TD></TD>
 132 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
 133 <TR><TD ALIGN=RIGHT> <b><tt>-xyinit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> Resize factor for the protein in the xy dimension before starting embedding </TD></TD>
 134 <TR><TD ALIGN=RIGHT> <b><tt>-xyend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Final resize factor in the xy dimension </TD></TD>
 135 <TR><TD ALIGN=RIGHT> <b><tt>-zinit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Resize factor for the protein in the z dimension before starting embedding </TD></TD>
 136 <TR><TD ALIGN=RIGHT> <b><tt>-zend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Final resize faction in the z dimension </TD></TD>
 137 <TR><TD ALIGN=RIGHT> <b><tt>-nxy</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1000</tt> </TD><TD> Number of iteration for the xy dimension </TD></TD>
 138 <TR><TD ALIGN=RIGHT> <b><tt>-nz</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of iterations for the z dimension </TD></TD>
 139 <TR><TD ALIGN=RIGHT> <b><tt>-rad</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.22  </tt> </TD><TD> Probe radius to check for overlap between the group to embed and the membrane </TD></TD>
 140 <TR><TD ALIGN=RIGHT> <b><tt>-pieces</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center. </TD></TD>
 141 <TR><TD ALIGN=RIGHT> <b><tt>-[no]asymmetry</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked. </TD></TD>
 142 <TR><TD ALIGN=RIGHT> <b><tt>-ndiff</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet. </TD></TD>
 143 <TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Maximum number of warning allowed </TD></TD>
 144 <TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
 145 <TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Be loud and noisy </TD></TD>
 146 </TABLE>
 147 <P>
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