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trj_cavity finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. The program works with files in PDB format, but it also can read/generate GROMACS compatible formats such as XTC.

The same project can be compiled as a GROMACS tool or as a standalone version. Installation instructions are provided in the INSTALL file of the project and in

If you need support using this tool (or report bugs), please post it in the discussion forum.

Remarks: v2 runs in parallel and supports GROMACS v5.1+ series. If you want to continue on using GROMACS v4.x, please use trj_cavity_v1.1.

trj_cavity Web Site




  • Finds protein cavities in MD simulation trajectories.
  • Produces MD trajectories of protein cavities vs time.
  • Provides statistics of protein cavity distribution.
  • Calculates cavity volume descriptor.
  • Normal axis pore tunnel radius profile.


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  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    bipinsingh, I have moved your review to the discussion forum since this page doesn't allow me to reply to reviews. Many thanks for your comments!

    Posted 04/02/2014
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    I have two commnets: (1) As mentioned in the abstract of the JCTC paper that stand-alone, GROMACS-independent version is also available at the same address, but could not locate the same. Can you please help me in this regard. (2) I tried the trj_cavity on my system after compiling the source code but it result in following error: "Segmentation fault (core dumped)" Please give your suggestions.

    Posted 03/31/2014
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