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

XAvier Periole x.periole at rug.nl
Fri Nov 6 14:25:33 CET 2009

> no, it does not work. the bilayer still "expands" along the periodic  
> boxes in the xy plane.
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).
> This probably means that the -pbc mol is not working properly to put  
> the lipids back in the box? The water molecules seem to be perfectly  
> well in place though. The commands being used are:
> echo 0 |   trjconv -f original.xtc -o pbcnojump.xtc -s bilayer.tpr - 
> n bilayer.ndx -pbc nojump
> echo 4 0 | trjconv -f pbcnojump.xtc -o center.xtc -s bilayer.tpr -n  
> bilayer.ndx -center
> echo 0 |   trjconv -f center.xtc -o pbcmol.xtc -s bilayer.tpr -n  
> bilayer.ndx -pbc mol
This should work! Or I am missing a big thing!
> group 4 contains all lipids, group zero contains the system. The  
> reference structure has the bilayer at the center of the box. the  
> origin ( 0 0 0 ) is at one box corner.
>> 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?
There is confusion here ...
-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

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