Well, Xavier :). I will give it one more shot, and get back to the list next week !<br><br><div class="gmail_quote">On Fri, Nov 6, 2009 at 4:45 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote></div>
Ok, what you describe does not make sense, not that you do not make<br>
sense but the fact that the lipids dot not come back to the central cell<br>
in the xy plan does not make sense!<br>
I really do not see why that could be! Never seen it ...<br>
<br>
In most cases for membrane proteins the problem of cutting molecules<br>
comes from the xy plan not the z direction.<br>
<br>
If I were you I would check for a last time your tpr file to make sure it is<br>
indeed what you think it is and it is fine ... erase all files and redo the<br>
all process, something went bad at some point.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
<br>
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).<br>
<br>
<br>
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>
<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>
<br>
-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>
<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>
<br></div></div><div class="im">
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