Processing tools for Gaussian AIMD
Just Got Here
7:04:51 AM PST - Sat, Jan 28th 2017
Dear NWChem users and developers

Recently, I noticed that the new version of NWChem has a new ability to compute ab initio molecular dynamics for finite systems using gaussian basis sets.
This feature is very promising for me and I appropriate the work of Fischer and his coworkers, but unfortunately there are only a few tools for processing the output of MD.
Is there any way to analyze the trajectory data with the tools of other codes such as GROMACS?

Regards
Hossein Hajiabadi
University of Sistan and Baluchestan

Forum Regular
7:01:03 AM PST - Mon, Jan 30th 2017
In order to use the tools from other programs you would need to convert the output from NWChem into a format that the other program can read. For instance, GROMACS usually wants its trajectory files in trr, xtc, or pdb format so you would need to convert the xyz file that NWChem produces to one of those formats. CatDCD is one potential way to do this conversion (http://www.ks.uiuc.edu/Development/MDTools/catdcd/)

Just Got Here
11:20:12 PM PST - Tue, Jan 31st 2017
Thank Sean
I hope this works, but can I ask you to tell me what is nwchem trajectory (xyz) file format is based on? Is it based on another MD software trajectory format or you created a new proprietary file format?

Forum Regular
7:02:14 AM PST - Wed, Feb 1st 2017
An xyz file is a fairly common chemical file format (https://en.wikipedia.org/wiki/XYZ_file_format).

NWChem produces a slightly modified version in that the atomic velocities are included along with the coordinates so that there three additional columns. The coordinates are given in angstroms and the velocities are given in angstroms/femtosecond. The addition of the additional columns specifying the velocities often doesn't cause any problems for programs that read xyz files as they usually just ignore any information on a line past the three coordinates.


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