no, it does not work. the bilayer still "expands" along the periodic boxes in the xy plane. <br><br>This probably means that the -pbc mol is not working properly to put the lipids back in the box? The water molecules seem to be perfectly well in place though. The commands being used are:<br>
<br>echo 0 | trjconv -f original.xtc -o pbcnojump.xtc -s bilayer.tpr -n bilayer.ndx -pbc nojump<br>echo 4 0 | trjconv -f pbcnojump.xtc -o center.xtc -s bilayer.tpr -n bilayer.ndx -center<br>echo 0 | trjconv -f center.xtc -o pbcmol.xtc -s bilayer.tpr -n bilayer.ndx -pbc mol<br>
<br>group 4 contains all lipids, group zero contains the system. The reference structure has the bilayer at the center of the box. the origin ( 0 0 0 ) is at one box corner. <br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Well you can see the bilayer as protein complex where each monomer is<br> a leaflet. Applying -pbc nojump on the trajectory would simply keep the two<br> leaflets together. Then the system can be centered using the bilayer as<br>
reference: this would put the bilayer at the center of the z axis. The<br> movements<br> "out of the box" can then be corrected using -pbc mol.<br> It is trivial is the reference structures are correct.<br> </blockquote>
</blockquote></div></blockquote></div></blockquote></div></div></div></div></blockquote></div><br>I do not think this is the case. In a protein complex, each monomer is bonded to the next amino acid, and therefore -pbc mol works, because the entire protein is a single molecule . In lipids however, why would trjconv treat the leaflet as a monomer?<br>