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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 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 <tt>g_membed</tt> embeds a membrane protein into an equilibrated lipid bilayer at the position
  18 and orientation specified by the user.<p>
  19 SHORT MANUAL<br>------------<br>
  20 The user should merge the structure files of the protein and membrane (+solvent), creating a
  21 single structure file with the protein overlapping the membrane at the desired position and
  22 orientation. The box size is taken from the membrane structure file. The corresponding topology
  23 files should also be merged. Consecutively, create a <tt>.<a href="tpr.html">tpr</a></tt> file (input for <tt>g_membed</tt>) from these files,with the following options included in the <tt>.<a href="mdp.html">mdp</a></tt> file.<br>
  24  - <tt>integrator      = md</tt><br>
  25  - <tt>energygrp       = Protein</tt> (or other group that you want to insert)<br>
  26  - <tt>freezegrps      = Protein</tt><br>
  27  - <tt>freezedim       = Y Y Y</tt><br>
  28  - <tt>energygrp_excl  = Protein Protein</tt><br>
  29 The output is a structure file containing the protein embedded in the membrane. If a topology
  30 file is provided, the number of lipid and
  31 solvent molecules will be updated to match the new structure file.<br>
  32 For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.<p>
  33 SHORT METHOD DESCRIPTION<br>
  34 ------------------------<br>
  35 1. The protein is resized around its center of mass by a factor <tt>-xy</tt> in the xy-plane
  36 (the membrane plane) and a factor <tt>-z</tt> in the <it>z</it>-direction (if the size of the
  37 protein in the z-direction is the same or smaller than the width of the membrane, a
  38 <tt>-z</tt> value larger than 1 can prevent that the protein will be enveloped by the lipids).<br>
  39 2. All lipid and solvent molecules overlapping with the resized protein are removed. All
  40 intraprotein interactions are turned off to prevent numerical issues for small values of <tt>-xy</tt>
  41  or <tt>-z</tt><br>
  42 3. One md step is performed.<br>
  43 4. The resize factor (<tt>-xy</tt> or <tt>-z</tt>) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the
  44 protein is resized again around its center of mass. The resize factor for the xy-plane
  45 is incremented first. The resize factor for the z-direction is not changed until the <tt>-xy</tt> factor
  46 is 1 (thus after <tt>-nxy</tt> iterations).<br>
  47 5. Repeat step 3 and 4 until the protein reaches its original size (<tt>-nxy</tt> + <tt>-nz</tt> iterations).<br>
  48 For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.<p>
  49 NOTE<br>----<br>
  50  - Protein can be any molecule you want to insert in the membrane.<br>
  51  - It is recommended to perform a short equilibration run after the embedding
  52 (see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly
  53 protein equilibration might require longer.<p>
  54 <P>
  55 <H3>Files</H3>
  56 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  57 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  58 <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>
  59 <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>
  60 <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>
  61 <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>
  62 <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>
  63 <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>
  64 <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>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-dat</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">  membed.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
  66 </TABLE>
  67 <P>
  68 <H3>Other options</H3>
  69 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  70 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  73 <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>
  74 <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>
  75 <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>
  76 <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>
  77 <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>
  78 <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>
  79 <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>
  80 <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>
  81 <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>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-[no]asymmetry</tt></b> </TD><TD ALIGN=RIGHT> 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>
  83 <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>
  84 <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>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-[no]start</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Call <a href="mdrun.html">mdrun</a> with membed options </TD></TD>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Be loud and noisy </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-mdrun_path</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Path to the <a href="mdrun.html">mdrun</a> executable compiled with this g_membed version </TD></TD>
  88 </TABLE>
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