Messages

1

MD simulations / Re: about "curavture" and "tangent" in dnaMD

« on: November 08, 2017, 12:02:40 pm »

Hi,

As written in tutorial (http://do-x3dna.readthedocs.io/en/latest/notebooks/helical_axis_tutorial.html), axis coordinate is determined using two base-pairs (one base-step) by 3DNA. Therefore, number of helical-axis coordinates is less than one of total number of base-pairs.

Unit of helical-axis is A, therefore, curvature unit is (1/A). Tangents are a list of vectors with same as helical-axis unit.

With regards,
Rajendra

2

MD simulations / Re: local helical axis vector for strongly bent DNA

« on: November 01, 2017, 06:41:45 am »

Hello,

I would like to point out that do_x3dna contains -ref option, which executes find_pair for only first frame, and same base-pairs information is used for whole trajectory. It is written in this link: http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html#ref.

With best regards,
Rajendra

3

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

4

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

« on: April 09, 2015, 06:28:49 am »

Hello,

Now an application note is online for do_x3dna in Bioinformatics (http://bioinformatics.oxfordjournals.org/content/early/2015/04/01/bioinformatics.btv190.short).

If you are using do_x3dna tool, please cite both 3DNA and do_x3dna papers.

Thank you very much.

Hi Xiang-Jun, Thank you very much for your support.

With best regards,
Rajendra

5

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

« on: January 12, 2015, 08:51:47 am »

Hi Xiang-Jun,

Thank you very much for your reply. In some of the publications, sum of rise was considered to be the contour length of the DNA. However, when I used rise/twist to calculate some quantities, MD simulations did not reproduce these quantities with experiments (optical tweezers and AFM). These quantities were calculated using contour length, which was directly measured in these experiments. In contrast, when I used helical-rise/-twist, these quantities are exactly reproducible with experiments. How would I explain this discrepancy? Any comment would be helpful.

I have also observed that the coordinates of local helical axis that are calculated from 3DNA, are very noisy (fluctuating) during MD simulations. If the helical-rise is calculated from local helical axis, sum of helical-rise is larger than the contour-length. For example, as depicted in the attached figure, length of red-curve (position of local helical axis from 3DNA) is larger than the blue-curve (smoothed helical axis).

Thank you very much in advance.

with best regards,
Rajendra

6

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

7

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

« on: September 03, 2014, 10:53:31 am »

Hello,

I have now made a new website for do_x3dna (http://rjdkmr.github.io/do_x3dna). This website contains detailed documentation for do_x3dna program and Python APIs.

Documentation for Python API is now available (http://rjdkmr.github.io/do_x3dna/apidoc.html).

Few tutorials about the Python APIs are also now available (http://rjdkmr.github.io/do_x3dna/tutorial.html).

Thanks.

With best regards,
Rajendra

8

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

9

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

« on: October 21, 2013, 06:47:08 am »

Thank you very much for reply.

It'd be great if you can test and verify that it works for "MD trajectory such as AMBER, NAMD and CHARMM".

I don't have trajectory from these MD packages, but recent GROMACS tools can read any type of trajectories which are supported by VMD.

If done right, a Python API on top of the wrapper will make the results of MD simulations readily accessible to a much larger community. I'd suggest you start from a small selection of key parameters, and build your tool incrementally.

I have been writing with the same intentions. I have chosen PYTHON because one can use NumPy/SciPy to perform calculations on raw data and Matplotlib to render plots of the obtained results. In future, I will do documentation for these APIs.

3DNA is composed of a few standalone commandline tools, and does not include a C APIs/library. However, I'd like to help you out where appropriate.

I was thinking that if I will able to pass coordinates and base-pair information directly to some C functions present in analyze, which in results would return all calculated parameters. At least, I can avoid writing and reading intermediate PDB files, and this process will speedup the wrapper execution.

Do you really need to run find_pair for each frame? See the output from running "x3dna_ensemble analyze -h".

I have implemented two type of calculations. In first type,  find_pair executes only once at the start, and then same base-pairs information is used for whole calculation. However, during simulations, new base-pair may form and old may break, particularly in RNA. Therefore in second type, find_pair  executes at every frame, and output files are generated such that, one can easily able to get how base-pairs are forming and breaking.

GitHub seems a good option. As for publishing such work, did you know the paper "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data" by Daniel Roe and Thomas Cheatham?

Thank you for the suggestions and paper reference.


With best regards,
Rajendra

10

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.