Thanks Tsjerk, I figured as much, but wanted to make sure I wasn't overlooking
something...
Take care,
Pablo
Hi Pablo,
You want to mutually exclusive things. That is by definition impossible.
Sorry,
Tsjerk
On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne <p.englebie...@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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