1 .TH g_membed 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_membed - embeds a protein into a lipid bilayer
8 .BI "\-f" " into_mem.tpr "
9 .BI "\-n" " index.ndx "
10 .BI "\-p" " topol.top "
11 .BI "\-o" " traj.trr "
12 .BI "\-x" " traj.xtc "
13 .BI "\-cpi" " state.cpt "
14 .BI "\-cpo" " state.cpt "
15 .BI "\-c" " membedded.gro "
16 .BI "\-e" " ener.edr "
18 .BI "\-ei" " sam.edi "
19 .BI "\-rerun" " rerun.xtc "
20 .BI "\-table" " table.xvg "
21 .BI "\-tablep" " tablep.xvg "
22 .BI "\-tableb" " table.xvg "
23 .BI "\-dhdl" " dhdl.xvg "
24 .BI "\-field" " field.xvg "
25 .BI "\-table" " table.xvg "
26 .BI "\-tablep" " tablep.xvg "
27 .BI "\-tableb" " table.xvg "
28 .BI "\-rerun" " rerun.xtc "
29 .BI "\-tpi" " tpi.xvg "
30 .BI "\-tpid" " tpidist.xvg "
31 .BI "\-ei" " sam.edi "
32 .BI "\-eo" " sam.edo "
33 .BI "\-j" " wham.gct "
34 .BI "\-jo" " bam.gct "
35 .BI "\-ffout" " gct.xvg "
36 .BI "\-devout" " deviatie.xvg "
37 .BI "\-runav" " runaver.xvg "
38 .BI "\-px" " pullx.xvg "
39 .BI "\-pf" " pullf.xvg "
40 .BI "\-mtx" " nm.mtx "
41 .BI "\-dn" " dipole.ndx "
42 .BI "\-multidir" " rundir "
44 .BI "\-[no]version" ""
46 .BI "\-deffnm" " string "
48 .BI "\-xyinit" " real "
49 .BI "\-xyend" " real "
50 .BI "\-zinit" " real "
55 .BI "\-pieces" " int "
56 .BI "\-[no]asymmetry" ""
58 .BI "\-maxwarn" " int "
59 .BI "\-[no]compact" ""
62 \&\fB g_membed\fR embeds a membrane protein into an equilibrated lipid bilayer at the position
63 \&and orientation specified by the user.
67 \-\-\-\-\-\-\-\-\-\-\-\-
69 \&The user should merge the structure files of the protein and membrane (+solvent), creating a
70 \&single structure file with the protein overlapping the membrane at the desired position and
71 \&orientation. The box size is taken from the membrane structure file. The corresponding topology
72 \&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.
74 \& \- \fB integrator = md\fR
76 \& \- \fB energygrp = Protein\fR (or other group that you want to insert)
78 \& \- \fB freezegrps = Protein\fR
80 \& \- \fB freezedim = Y Y Y\fR
82 \& \- \fB energygrp_excl = Protein Protein\fR
84 \&The output is a structure file containing the protein embedded in the membrane. If a topology
85 \&file is provided, the number of lipid and
86 \&solvent molecules will be updated to match the new structure file.
88 \&For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169\-2174, Appendix.
91 \&SHORT METHOD DESCRIPTION
93 \&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
95 \&1. The protein is resized around its center of mass by a factor \fB \-xy\fR in the xy\-plane
96 \&(the membrane plane) and a factor \fB \-z\fR in the \fI z\fR\-direction (if the size of the
97 \&protein in the z\-direction is the same or smaller than the width of the membrane, a
98 \&\fB \-z\fR value larger than 1 can prevent that the protein will be enveloped by the lipids).
100 \&2. All lipid and solvent molecules overlapping with the resized protein are removed. All
101 \&intraprotein interactions are turned off to prevent numerical issues for small values of \fB \-xy\fR
104 \&3. One md step is performed.
106 \&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
107 \&protein is resized again around its center of mass. The resize factor for the xy\-plane
108 \&is incremented first. The resize factor for the z\-direction is not changed until the \fB \-xy\fR factor
109 \&is 1 (thus after \fB \-nxy\fR iterations).
111 \&5. Repeat step 3 and 4 until the protein reaches its original size (\fB \-nxy\fR + \fB \-nz\fR iterations).
113 \&For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169\-2174.
119 \& \- Protein can be any molecule you want to insert in the membrane.
121 \& \- It is recommended to perform a short equilibration run after the embedding
122 \&(see Wolf et al, J Comp Chem 31 (2010) 2169\-2174), to re\-equilibrate the membrane. Clearly
123 \&protein equilibration might require longer.
127 .BI "\-f" " into_mem.tpr"
129 Run input file: tpr tpb tpa
131 .BI "\-n" " index.ndx"
135 .BI "\-p" " topol.top"
139 .BI "\-o" " traj.trr"
141 Full precision trajectory: trr trj cpt
143 .BI "\-x" " traj.xtc"
145 Compressed trajectory (portable xdr format)
147 .BI "\-cpi" " state.cpt"
151 .BI "\-cpo" " state.cpt"
155 .BI "\-c" " membedded.gro"
157 Structure file: gro g96 pdb etc.
159 .BI "\-e" " ener.edr"
167 .BI "\-ei" " sam.edi"
171 .BI "\-rerun" " rerun.xtc"
173 Trajectory: xtc trr trj gro g96 pdb cpt
175 .BI "\-table" " table.xvg"
179 .BI "\-tablep" " tablep.xvg"
183 .BI "\-tableb" " table.xvg"
187 .BI "\-dhdl" " dhdl.xvg"
191 .BI "\-field" " field.xvg"
195 .BI "\-table" " table.xvg"
199 .BI "\-tablep" " tablep.xvg"
203 .BI "\-tableb" " table.xvg"
207 .BI "\-rerun" " rerun.xtc"
209 Trajectory: xtc trr trj gro g96 pdb cpt
211 .BI "\-tpi" " tpi.xvg"
215 .BI "\-tpid" " tpidist.xvg"
219 .BI "\-ei" " sam.edi"
223 .BI "\-eo" " sam.edo"
227 .BI "\-j" " wham.gct"
229 General coupling stuff
231 .BI "\-jo" " bam.gct"
233 General coupling stuff
235 .BI "\-ffout" " gct.xvg"
239 .BI "\-devout" " deviatie.xvg"
243 .BI "\-runav" " runaver.xvg"
247 .BI "\-px" " pullx.xvg"
251 .BI "\-pf" " pullf.xvg"
255 .BI "\-mtx" " nm.mtx"
259 .BI "\-dn" " dipole.ndx"
263 .BI "\-multidir" " rundir"
264 .B Input, Opt., Mult.
269 Print help info and quit
271 .BI "\-[no]version" "no "
272 Print version info and quit
274 .BI "\-nice" " int" " 0"
277 .BI "\-deffnm" " string" " "
278 Set the default filename for all file options
280 .BI "\-xvg" " enum" " xmgrace"
281 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
283 .BI "\-xyinit" " real" " 0.5 "
284 Resize factor for the protein in the xy dimension before starting embedding
286 .BI "\-xyend" " real" " 1 "
287 Final resize factor in the xy dimension
289 .BI "\-zinit" " real" " 1 "
290 Resize factor for the protein in the z dimension before starting embedding
292 .BI "\-zend" " real" " 1 "
293 Final resize faction in the z dimension
295 .BI "\-nxy" " int" " 1000"
296 Number of iteration for the xy dimension
298 .BI "\-nz" " int" " 0"
299 Number of iterations for the z dimension
301 .BI "\-rad" " real" " 0.22 "
302 Probe radius to check for overlap between the group to embed and the membrane
304 .BI "\-pieces" " int" " 1"
305 Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center.
307 .BI "\-[no]asymmetry" "no "
308 Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked.
310 .BI "\-ndiff" " int" " 0"
311 Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet.
313 .BI "\-maxwarn" " int" " 0"
314 Maximum number of warning allowed
316 .BI "\-[no]compact" "yes "
317 Write a compact log file
325 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.