[gmx-users] Continuous trajectory from trjconv?
p.englebienne at tue.nl
Mon Mar 1 11:02:08 CET 2010
Hi, I made an NpT MD simulation of 10 copies of the same small molecule
in CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualize the
evolution of the system and the distance between the molecules. I tried
to visualize the system, but I can't get a continuous trajectory (i.e.,
without jumps) without the solutes diffusing out of the simulation box.
The same thing happens for the inter-molecule distance, it oscillates
wildly between a reasonable value (say, 0.5 nm) and 1/2 the size of the
When I use trjconv with the "-pbc nojump -ur compact" options, the
molecules diffuse out of the box, in a continuous trajectory, until they
are way further apart than the size of the cell. When visualizing it in
VMD, however, it turns out that not all molecules are isolated, but
instead some are interacting with the periodic image of another
molecule. I used "pbc wrap" from the PBCTools module within VMD and that
brings all the molecules into a single cell, but then the trajectory is
not continuous, with compounds jumping around the edges of the unit
cell. It is then not straightforward to see the interaction among
different molecules, as in some cases they are in opposite edges of the
If I use the "-pbc mol -ur compact" option, all molecules stay within a
single unit cell, but there are jumps across the border of the unit cell
as in the above case.
I tried also using the "-center", "-fit rot+trans" and "-fit
progressive" options (with groups containing either all molecules or a
single residue) but this ultimately gave the same results.
Would there be something else I could try to visualize the simulation so
that the central unit cell would contain all residues in a continuous way?
Thanks in advance for reading, and more for replying!
Pablo Englebienne, PhD
Institute of Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349
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