Do I need gromacs to use dnaMD for simulations?

[piia600]

Hi all,

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

[xiangjun]

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

Thanks for using DSSR and for posting your questions on the 3DNA Forum. As for the analysis of an ensemble, please see the DSSR manual , especially Section: "3.13 The --nmr option":

The DSSR --nmr (or --md) option automates the analysis of an ensemble, such as NMR structures in the PDB or snapshots from MD simulations. The input coordinates file must be in either the classic PDB format where each model is delineated by MODEL/ENDMDL tags, or the mmCIF format where each ATOM/HETATM record has an associated model number.
...
The --json option makes it easy to parse the output of multiple models pragmatically. In addition to NMR structures, trajectories from MD simulations can also be processed. Popular MD packages (AMBER, GROMACS, CHARMM, etc.) all have their own specialized binary formats for trajectories. By design, DSSR does not work on these binary files. They must be converted to the standard PDB or mmCIF format to be analyzed by DSSR. The combination of --nmr and --json makes DSSR directly accessible to the MD community.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

I am not a practitioner of MD simulations. Questions related to dnaMD are best answered by its developer: hopefully @rkumar will chime in. See the thread Update of do_x3dna package, which can be used with files generated by GROMACS.

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

There have been too many spam registrations nowadays, so I must stay continuously vigilant to keep the Forum clean. You should now see the download link. Sorry for the inconvenience.

Best regards,

Xiang-Jun

[rkumar]

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

No, dnaMD is a python package purely written in python. However, it requires output from do_x3dna,  which is now available for direct download and does not require GROMACS installation. You can use both do_x3dna and dnaMD without requiring GROMACS installation.

Thanks,

[piia600]

Thanks for the help!

Now I have managed to install both 3DNA and do_x3DNA for GROMACS. However, it seems do_x3DNA needs 'residuetypes.dat' file form GROMACS installation. It seems I was able to bypass this by downloading the file form github and putting it in the working folder. I thought you might want to put a note of this to the documentation.

Keep up the good work!