1g_membed(1) GROMACS suite, VERSION 4.5 g_membed(1)
2
6 g_membed - embeds a protein into a lipid bilayer
7 VERSION 4.5
9
11 g_membed -f into_mem.tpr -n index.ndx -p topol.top -o traj.trr -x
12 traj.xtc -cpi state.cpt -cpo state.cpt -c membedded.gro -e ener.edr -g
13 md.log -ei sam.edi -rerun rerun.xtc -table table.xvg -tablep tablep.xvg
14 -tableb table.xvg -dhdl dhdl.xvg -field field.xvg -table table.xvg
15 -tablep tablep.xvg -tableb table.xvg -rerun rerun.xtc -tpi tpi.xvg
16 -tpid tpidist.xvg -ei sam.edi -eo sam.edo -j wham.gct -jo bam.gct
17 -ffout gct.xvg -devout deviatie.xvg -runav runaver.xvg -px pullx.xvg
18 -pf pullf.xvg -mtx nm.mtx -dn dipole.ndx -[no]h -[no]version -nice int
19 -deffnm string -xvg enum -xyinit real -xyend real -zinit real -zend
20 real -nxy int -nz int -rad real -pieces int -[no]asymmetry -ndiff int
21 -maxwarn int -[no]compact -[no]v
22
24 g_membed embeds a membrane protein into an equilibrated lipid bilayer
25 at the position and orientation specified by the user.
26 SHORT MANUAL ------------
30 The user should merge the structure files of the protein and membrane
32 (+solvent), creating a single structure file with the protein overlap‐
33 ping the membrane at the desired position and orientation. Box size
34 should be taken from the membrane structure file. The corresponding
35 topology files should also be merged. Consecutively, create a tpr file
36 (input for g_membed) from these files,with the following options
37 included in the mdp file.
38 - integrator = md
40 - energygrp = Protein (or other group that you want to insert)
42 - freezegrps = Protein
44 - freezedim = Y Y Y
46 - energygrp_excl = Protein Protein
48 The output is a structure file containing the protein embedded in the
50 membrane. If a topology file is provided, the number of lipid and sol‐
51 vent molecules will be updated to match the new structure file.
52 For a more extensive manual see Wolf et al, J Comp Chem 31 (2010)
54 2169-2174, Appendix.
55 SHORT METHOD DESCRIPTION
59 ------------------------
61 1. The protein is resized around its center of mass by a factor -xy in
63 the xy-plane (the membrane plane) and a factor -z in the z-direction
64 (if the size of the protein in the z-direction is the same or smaller
65 than the width of the membrane, a -z value larger than 1 can prevent
66 that the protein will be enveloped by the lipids).
67 2. All lipid and solvent molecules overlapping with the resized protein
69 are removed. All intraprotein interactions are turned off to prevent
70 numerical issues for small values of -xy or -z
71 3. One md step is performed.
73 4. The resize factor (-xy or -z) is incremented by a small amount
75 ((1-xy)/nxy or (1-z)/nz) and the protein is resized again around its
76 center of mass. The resize factor for the xy-plane is incremented
77 first. The resize factor for the z-direction is not changed until the
78 -xy factor is 1 (thus after -nxy iteration).
79 5. Repeat step 3 and 4 until the protein reaches its original size
81 (-nxy + -nz iterations).
82 For a more extensive method descrition see Wolf et al, J Comp Chem, 31
84 (2010) 2169-2174.
85 NOTE ----
89 - Protein can be any molecule you want to insert in the membrane.
91 - It is recommended to perform a short equilibration run after the
93 embedding (see Wolf et al, J Comp Chem 31 (2010) 2169-2174, to re-equi‐
94 librate the membrane. Clearly protein equilibration might require
95 longer.
96
101 -f into_mem.tpr Input
102 Run input file: tpr tpb tpa
103 -n index.ndx Input, Opt.
105 Index file
106 -p topol.top In/Out, Opt.
108 Topology file
109 -o traj.trr Output
111 Full precision trajectory: trr trj cpt
112 -x traj.xtc Output, Opt.
114 Compressed trajectory (portable xdr format)
115 -cpi state.cpt Input, Opt.
117 Checkpoint file
118 -cpo state.cpt Output, Opt.
120 Checkpoint file
121 -c membedded.gro Output
123 Structure file: gro g96 pdb etc.
124 -e ener.edr Output
126 Energy file
127 -g md.log Output
129 Log file
130 -ei sam.edi Input, Opt.
132 ED sampling input
133 -rerun rerun.xtc Input, Opt.
135 Trajectory: xtc trr trj gro g96 pdb cpt
136 -table table.xvg Input, Opt.
138 xvgr/xmgr file
139 -tablep tablep.xvg Input, Opt.
141 xvgr/xmgr file
142 -tableb table.xvg Input, Opt.
144 xvgr/xmgr file
145 -dhdl dhdl.xvg Output, Opt.
147 xvgr/xmgr file
148 -field field.xvg Output, Opt.
150 xvgr/xmgr file
151 -table table.xvg Input, Opt.
153 xvgr/xmgr file
154 -tablep tablep.xvg Input, Opt.
156 xvgr/xmgr file
157 -tableb table.xvg Input, Opt.
159 xvgr/xmgr file
160 -rerun rerun.xtc Input, Opt.
162 Trajectory: xtc trr trj gro g96 pdb cpt
163 -tpi tpi.xvg Output, Opt.
165 xvgr/xmgr file
166 -tpid tpidist.xvg Output, Opt.
168 xvgr/xmgr file
169 -ei sam.edi Input, Opt.
171 ED sampling input
172 -eo sam.edo Output, Opt.
174 ED sampling output
175 -j wham.gct Input, Opt.
177 General coupling stuff
178 -jo bam.gct Output, Opt.
180 General coupling stuff
181 -ffout gct.xvg Output, Opt.
183 xvgr/xmgr file
184 -devout deviatie.xvg Output, Opt.
186 xvgr/xmgr file
187 -runav runaver.xvg Output, Opt.
189 xvgr/xmgr file
190 -px pullx.xvg Output, Opt.
192 xvgr/xmgr file
193 -pf pullf.xvg Output, Opt.
195 xvgr/xmgr file
196 -mtx nm.mtx Output, Opt.
198 Hessian matrix
199 -dn dipole.ndx Output, Opt.
201 Index file
202
205 -[no]hno
206 Print help info and quit
207 -[no]versionno
209 Print version info and quit
210 -nice int 0
212 Set the nicelevel
213 -deffnm string
215 Set the default filename for all file options
216 -xvg enum xmgrace
218 xvg plot formatting: xmgrace, xmgr or none
219 -xyinit real 0.5
221 Resize factor for the protein in the xy dimension before starting
222 embedding
223 -xyend real 1
225 Final resize factor in the xy dimension
226 -zinit real 1
228 Resize factor for the protein in the z dimension before starting
229 embedding
230 -zend real 1
232 Final resize faction in the z dimension
233 -nxy int 1000
235 Number of iteration for the xy dimension
236 -nz int 0
238 Number of iterations for the z dimension
239 -rad real 0.22
241 Probe radius to check for overlap between the group to embed and the
242 membrane
243 -pieces int 1
245 Perform piecewise resize. Select parts of the group to insert and
246 resize these with respect to their own geometrical center.
247 -[no]asymmetryno
249 Allow asymmetric insertion, i.e. the number of lipids removed from the
250 upper and lower leaflet will not be checked.
251 -ndiff int 0
253 Number of lipids that will additionally be removed from the lower
254 (negative number) or upper (positive number) membrane leaflet.
255 -maxwarn int 0
257 Maximum number of warning allowed
258 -[no]compactyes
260 Write a compact log file
261 -[no]vno
263 Be loud and noisy
264
267 gromacs(7)
268 More information about GROMACS is available at <http://www.gro‐
270 macs.org/>.
271 Thu 26 Aug 2010 g_membed(1)