[gmx-users] Continuous trajectory from trjconv?

Pablo Englebienne 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 
periodic cell.

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!

Take care,

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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