[gmx-users] Groove width

spss4 at iacs.res.in spss4 at iacs.res.in
Mon Jun 4 13:21:30 CEST 2018

  ----- Message from rajendra kumar <rjdkmr at gmail.com> ---------
    Date: Mon, 4 Jun 2018 12:23:56 +0200
    From: rajendra kumar <rjdkmr at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Groove width
      To: Discussion list for GROMACS users <gmx-users at gromacs.org>

>> I am doing simulation of DNA molecule. I want to calculate groove width
>> of
>> DNA in GROMACS. How to do this? Someone please help.
> ​You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in
> background and works with GROMACS files.​ Package also includes tools
> analyze the large data generated from MD trajectories.
> --
> Hii
> I have tried installation of do_x3dna in ubuntu system following the
> instructions given in the link. Installation done successfully then I
> have written the path of do_x3dna in .bashrc file(export
> do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
> Then I tried doing do_x3dna -h but it shows do_x3dna not found. What is
> wrong here? My GROMACS version is 2016.3 . Need suggestion .
> sunipa

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----- End message from rajendra kumar <rjdkmr at gmail.com> -----

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