[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 14:06:47 CET 2009

no, it does not work. the bilayer still "expands" along the periodic boxes
in the xy plane.

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

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?
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