[gmx-users] Re: Continuous trajectory from trjconv?

Pablo Englebienne p.englebienne at tue.nl
Mon Mar 1 12:54:53 CET 2010

Thanks Tsjerk, I figured as much, but wanted to make sure I wasn't overlooking something...

Take care,

Hi Pablo,

You want to mutually exclusive things. That is by definition impossible.



On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne <p.englebienne at tue.nl> wrote:

> 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 cell.
> 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?
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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