[gmx-users] Problem with trjconv and centering bilayer.

[Ioannis Beis]

Dear gromacs users,

I am trying to center the trajectory of a bilayer in the rectangular  
simulation box in the frame of my effort to calculate the bilayer  
thickness with g_dist. According to the visualization, the upper layer  
of the membrane lies on the lowest part of the box and the lower part  
of the membrane on the highest part of the box, with the water in the  
middle. There should not be anything wrong with drifting along the  
z-axis, since the initial structure was at the very bottom of the box,  
so even a small drift downwards -due to the pbc- would place the lower  
part of the membrane on the top of the box.

I tried issuing:

trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o  
my_trajectory_no_jump.xtc -pbc nojump

with 0 (for system) and subsequently

trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o  
my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol

with 1 (other) for centering and 0 (system) for output.

I used this kind of commands some time ago and they worked fine. Now  
strangely the bilayer remains around the position that I described in  
the beginning. Is it possible that the program treats the bilayer  
separated as it looks in vmd and considers the geometrical center in  
the middle of the water instead of the middle of the bilayer?

I tried the -trans flag to translate the bilayer along z-axis near the  
center and repeated the steps, but the new trajectory wasn't even  
visible in vmd. In addition, the .gro files generated by trjconv are  
apparently trajectory files instead of structure files. I don't feel  
confident about using editconf for operations like translation of a  
single initial structure, because as far as I understand editconf is a  
tool meant mostly for setting up systems; thus I was sceptical about  
messing a structure with editconf that I would later on use together  
with an .xtc file as input for trjconv.  However, trjconv doesn't seem  
to generate structure output files. I don't understand the meaning of  
a .gro file as trajectory file since there are already at least 3 file  
formats for trajectories.

So how can I bring my bilayer's trajectory in the center of the unit  
cell for reliable thickness calculation without drifts? Is it possible  
at the same time to have clear visualization without disturbances?  
trjconv with -pbc mol still gives rise to lines in the visualization,  
apparently as a result of atom jumps. Sadly trajectory files cannot be  
inspected and visualization is quite handy for certain types of  
feedback in various data analysis-related tasks, so it would be nice  
if the trajectories used for analysis also look proper in vmd.

Thank you in advance.

Best regards,
Ioannis