Ioannis Beis wrote:
Quoting gmx-users-requ...@gromacs.org:
Message: 2
Date: Mon, 16 Jan 2012 13:38:11 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Problem with trjconv and centering bilayer.
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4f146e93.4090...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
Ioannis Beis wrote:
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?
That's exactly what it does.
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.
Generally speaking, a trajectory is just a series of coordinates, so
you can
output it into a number of formats, including .gro and .pdb, among
others. You
get a chain of coordinate files that may (or may not) end up being
useful in
some applications.
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.
I can think of two approaches, the first of which I have used so it
should work ;)
1. Provide a custom index group specifying only a single lipid atom
from the end
of a hydrocarbon chain and center on it. Therefore, its geometric
center has to
be the center of the box, and it should bring the rest of the membrane
to the
(visual) center of the unit cell.
2. Calculate the distance with the trajectory you have now, and
subtract it from
the z-length (assuming the membrane plane is x-y) of the box (stored
in the .edr
file).
First of all thank you very much for the reply. To make sure there is
not something that I misunderstand about how trjconv works, I would like
to mention what I did and how I anticipate it.
I made the index file with a last carbon from a random acyl chain and
issued:
trjconv -f my_init_traj.xtc -o towards_center_traj.xtc -pbc mol -center
-boxcenter tric -n tip_atom.ndx
How did this work? The use of -pbc implies the need for -s.
with centering at the index file atom and then:
trjconv -f towards_center_traj.xtc -s my_binary.tpr -o centered_traj.xtc
-pbc mol -center -boxcenter tric
If properly centered, this step should not be required.
with centering at the middle of the bilayer. The final .xtc output is to
be used as input in the g_dist.
I assume that .tpr is used only for the masses of the atoms (so we are
talking about a mass-weighted geometrical center, which isn't mentioned
in the manual). Therefore it is mandatory in the second command, but not
in the first. Is this going to give the correct result?
Masses are not used for centering; it is a simple coordinate transformation.
See the center_x routine in gmx_trjconv.c.
A relevant concern is whether the -pbc flag is used properly. I just
used the mol value assuming that is appropriate for this context (is it
necessary?). Does it make any difference in the results if I use -pbc
nojump or no -pbc at all in the first command? To be honest, I do not
understand well the pbc treatment of trjconv. For example it is not
clear who is translated where exactly and certain options imply
modification of the size of the box. Is there a clear description
somewhere? The manual is confusing. In most cases one uses the original
trajectory, but it is important to know what does what in pbc for
certain tasks.
Without a bit more suggestion, it's hard to know how to improve the
documentation. Those of us who maintain it are always happy to improve it, but
I'm sorry to say "it's confusing" doesn't give much of a sense of how it might
be made more useful.
In this procedure, the use of -pbc may not even be necessary at all. Try a
simple centering operation with your custom index group and see if the results
are satisfactory. If not, we'll have to work based off of the result.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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