Hi Daniel,
1a. I am confused about what is your vesicle. Is it everything that
you are showing in these images? Or perhaps it is only the cyan thing
that I can see sliced through in:
http://img109.imageshack.us/img109/8227/trajenddat.jpg
1b. I suspect that the cyan ring encircled by green in the above
mentioned image is actually the beginning of a pbc-merger event of
your vesicle with itself. If this is true, then definitely refer to
point 2 below. This would be easier to see if you create an image of
the trajenddat.jpg in which you display a number of periodic images.
2. In addition to what Tsjerk has mentioned, your might need a larger
simulation box in order to simulate your vesicle properly. If it is
actually interacting with itself then you may be sampling a state that
is actually uninteresting to you. At the very least, it is more
complex than it needs to be.
Regarding the rebuilding procedure that Tsjerk has mentioned, we are
in the process of coding this functionality into gromacs. I believe
that Berk also has a slightly different solution here. Nevertheless,
no amount of pbc finessing is going to change the fact that you are
simulating a state that appears to be different than what you are
interested in.
Chris.
-- original message --
Hi Daniel,
The problem is likely that your vesicle is interacting with itself
over the periodic boundaries. There are regions where there is no
solvent inbetween. That means that lipids can go over from one image
to the other by diffusion, which will not be compensated by using -pbc
nojump. You seem to be out of luck there.
The solution to solve this problem would be to rebuild the vesicle by
minimizing the sum of squared deviations from the center using shifts
over the lattice. But that is not implemented.
Cheers,
Tsjerk
On Tue, Dec 1, 2009 at 2:55 PM, Daniel Parton
<daniel.parton at bioch.ox.ac.uk> wrote:
Hi,
I've tried using trjconv -pbc nojump with a .tpr created from the first
frame of the trajectory (clustered so the vesicle should be whole). The
output trajectory starts with a complete vesicle, but small numbers of lipid
particles progressively move to places outside of the box. By the end of the
trajectory there appear to be 8 groups of particles outside the box, which
have the same overall spherical shape as the vesicle, but are comprised of
only a few hundred particles. I have uploaded some pictures here:
http://img109.imageshack.us/g/trajenddat.jpg/
traj-start is the first frame of the unprocessed trajectory:
http://img40.imageshack.us/img40/2181/trajstartdat.jpg
traj-end is the last frame of the unprocessed trajectory:
http://img109.imageshack.us/img109/8227/trajenddat.jpg
nojump-start is the first frame of the trajectory following trjconv -pbc
nojump, as described above. The vesicle starts whole:
http://img138.imageshack.us/img138/4531/nojumpstartdat.jpg
nojump-end is the last frame of the trajectory following trjconv -pbc
nojump. Note that some particles have moved to being outside the box,
seeming to take up space resembling 8 copies of the vesicle system.
http://img689.imageshack.us/img689/2821/nojumpenddat.jpg
0ns-cluster is the first frame of the trajectory, clustered using trjconv
-pbc cluster. The pbc option may have gone a bit wrong? Particles which
should be very close to the box boundary seem to have been moved to other
places in or outside the box. Other parts which lie some way inside or
outside the box appear (correctly) as part of the vesicle:
http://img222.imageshack.us/img222/4268/0nsclusterdat.jpg
So I am wondering the problem lies with the 0ns-cluster system. As some
particles are not part of the vesicle in this representation, this could
explain why some particles are not being counted as part of the vesicle by
trjconv -pbc nojump. Does this seem likely, and has anyone seen similar
behaviour to that seen in 0ns-cluster, where trjconv -pbc cluster has been
used with a rhombic dodecahedron box?
Many thanks for all of your help so far,
Daniel
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