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

[XAvier Periole]

On Nov 6, 2009, at 5:32 PM, maria goranovic wrote:

> Well, Xavier :). I will give it one more shot, and get back to the  
> list next week !
I'll be away for a while ... good luck.
>
> On Fri, Nov 6, 2009 at 4:45 PM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> 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)
>
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>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
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