Well .. I mean .. the lipids are not put back into the central simulation cell in the xy plane. so they keep the nojump effect<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;">
what do you mean "expand"? They do not get back in the box meaning they keep the nojump<br>
effect or it is just that they have the tail out of the box?<br>
-pbc mol will put the COM of the molecule (protein/lipid/water ...) in the box and leave the molecule<br>
as a whole (no cutting bonds).<div class="im"><br>
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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>
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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>
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-pbc mol will work on each molecule, see above, but not on the lipid bilayer of course.<br>
This is why you use nojump first! and then center ... then the lipid molecules will be put<br>
in the box on the xy plan but not across the z axis<br><div><div class="h5"></div></div></blockquote><div><br>And -pbc nojump will also work on each molecule, not on a leaflet as a whole.<br><br>I think the following takes place:<br>
<br>The bilayer moves along -z, and some lipids eventually leave the box on one edge, and appear on the other edge. -pbc nojump ensures that the lipids do not do this, and instead continue drifting along -z. thus the center of mass of the lipids should just keep moving along -z after using -pbc nojump. It is therefore easy to correct this drift while using -center. <br>
<br>However, the lipids also diffuse in the x and the y direction, but this diffusion is random. THIS TOO, is changed by using -pbc nojump. Thus, pbc nojump changes the center of mass behavior of the lipids in all three directions. It can be corrected for z, because the z-drift is always along one direction (all lipids diffuse either in -z or +z), but cannot be corrected for xy, because individual lipids diffuse randomly (both along +x/y or -x/y)<br>
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