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
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