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

maria goranovic mariagoranovic at gmail.com
Fri Nov 6 15:09:25 CET 2009

Well .. I mean .. the lipids are not put back into the central simulation
cell in the xy plane. so they keep the nojump effect

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

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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