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Questions and answers > MD simulations
do_x3dna as a plugin for VMD and update in dnaMD
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Rajendra Kumar:
Hello,
I have developed do_x3dna as a plugin for VMD (http://do-x3dna.readthedocs.io/en/latest/vmd_plugin.html). Now, two variants of do_x3dna are available, one for GROMACS and other as a plugin for VMD.
Now dnaMD can be used as both Python module (http://do-x3dna.readthedocs.io/en/latest/api_summary.html)) and command line tools (http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html). I am still expanding the dnaMD command. dnaMD can be installed easily through pip (http://do-x3dna.readthedocs.io/en/latest/install_dnaMD.html).
With best regards,
Rajendra
xiangjun:
Hi Rajendra,
Nice effort! Now do_x3dna and 3DNA are reaily accessible to the huge VMD user community.
Thanks for keep us informed of your new progress!
Xiang-Jun
Beñat Olave:
Dear Rajendra,
We are a group from Spain, our research is focused in creating different functional DNA nanostructures.
We have just started using computational chemistry and after doing some MD simulations I wanted to study the trajectories of a dsDNA using your tool, I think it can provide very useful information.
Unfortunately, I had issues while installing its plugin for VMD in windows 10 (x86). Even if it seems it is correctly installed:
"package require do_x3dna
1.0"
When I execute any command "do_x3dna WHATEVER", it closes immediately.
I have just solved the closure deleting all the "exit" words from the script but it still gives me this error:
=================== ERROR ======================
$X3DNA environment variable is not available.
See below for usage.
================================================
I don't understand why, because I have already installed X3DNA correctly, I have used it for other analysis of a single step.
Could you help me?
Best regards,
Beñat Olave
xiangjun:
Dear Beñat,
As a follow-up, I sent Rajendra an email message on May 2, asking him if he is still in support of do_x3dna. As with your questions here, I've so far not heard back from Rajendra. Based on my previous experience, I know he is very responsive. So, he may no longer support do_x3dna.
Best regards,
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.