Topics

1

MD simulations / do_x3dna as a plugin for VMD and update in dnaMD

« on: November 01, 2017, 06:16:55 am »

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

2

General discussions (Q&As) / difference between rise/twist and helical-rise/twist

« on: January 08, 2015, 08:51:12 am »

Hello,

I would like to know difference between rise/twist and helical-rise/-twist. For example, if I would like to calculate contour length of the long DNA, whether sum of rise or sum of helical-rise would give the contour length of the entire DNA.

Thank you very much in advance.

With best regards,
Rajendra

3

MD simulations / do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories

« on: July 09, 2014, 06:46:33 am »

Hello,

As discussed in this thread (http://forum.x3dna.org/related-topics/wrapper-for-gromacs-md-trajectroy/), now, do_x3dna (https://github.com/rjdkmr/do_x3dna) package is available for download and installation.

I am still working on the Python-APIs, which enable the user to perform specific analysis. Soon, I will upload a extensive tutorial for using these APIs.

Any suggestions would be very helpful to improve this package.

Thanks.

With best regards,
Rajendra

4

General discussions (Q&As) / Wrapper for GROMACS MD trajectroy

« on: October 16, 2013, 06:47:31 am »

Hello,

I have developed a 3DNA wrapper in C language, which uses GROMACS library to read GROMACS format trajectory, topology and index file. This wrapper dumps frame-wise data to several text files. I guess, this tool will work for any format of MD trajectory such as AMBER, NAMD and CHARMM, but it is yet to be tested.

Additionally, I am developing Python APIs to analyze the vast amount of data obtained from the wrapper. It includes many useful methods to analyze properties of the DNA. One can analyze the changes in DNA upon binding to protein. Also, it can be used to calculate elastic properties of the DNA. Moreover, I have implemented few methods to analyze bending motions of helical axis.

I have a query. Since I am using C language for wrapper, may I get C APIs/library of 3DNA such that I can use directly these APIs in wrapper. Currently, I use find_pair and analyze executable binary. When I use wrapper for ~30,000 frames containing 60 BP DNA, it takes a while to complete and I want to speed up this calculation.

I would like to release this tool through GitHub, however I am not sure that this work alone is of publication level. Please let me know, what would be your suggestion.

Thanks.