[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

[XAvier Periole]

> Well .. I mean .. the lipids are not put back into the central  
> simulation cell in the xy plane. so they keep the nojump effect
Ok, what you describe does not make sense, not that you do not make
sense but the fact that the lipids dot not come back to the central cell
in the xy plan does not make sense!
I really do not see why that could be! Never seen it ...

In most cases for membrane proteins the problem of cutting molecules
comes from the xy plan not the z direction.

If I were you I would check for a last time your tpr file to make sure  
it is
indeed what you think it is and it is fine ... erase all files and  
redo the
all process, something went bad at some point.

>
> what do you mean "expand"? They do not get back in the box meaning  
> they keep the nojump
> effect or it is just that they have the tail out of the box?
> -pbc mol will put the COM of the molecule (protein/lipid/water ...)  
> in the box and leave the molecule
> as a whole (no cutting bonds).
>
>
> Well you can see the bilayer as protein complex where each monomer is
> a leaflet. Applying -pbc nojump on the trajectory would simply keep  
> the two
> leaflets together. Then the system can be centered using the bilayer  
> as
> reference: this would put the bilayer at the center of the z axis. The
> movements
> "out of the box" can then be corrected using -pbc mol.
> It is trivial is the reference structures are correct.
>
> 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?
>
> -pbc mol will work on each molecule, see above, but not on the lipid  
> bilayer of course.
> This is why you use nojump first! and then center ... then the lipid  
> molecules will be put
> in the box on the xy plan but not across the z axis
>
> And -pbc nojump will also work on each molecule, not on a leaflet as  
> a whole.
>
> I think the following takes place:
>
> 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.
>
> 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)
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php