How to analyze .nc or .dcd trajectory files in GROMACS

User discussions
1

Respected Sir/Ma’am,
I am Sankar Maity, a Ph.D scholar at the National Institute of Technology Rourkela, India. I have .nc or .dcd trajectory files using AMBER and would like to perform further analysis (GROMACS-LS and the MDStress library enable the calculation of local stress fields from molecular dynamics simulations). Could anyone please suggest me on how to analyze my trajectory files (.nc or .dcd) using GROMACS?

Thank You
Sankar Maity

2

I would recommend using MDTraj: MDTraj — MDTraj 1.9.8.dev0 documentation to convert from .dcd to .xtc (or .trr). However, if you need a .tpr file for your analyses, it will not be as simple as that.

3

Respected sir,
Thank you sir for your guidance, successfully converted my .dcd files to .xtc files by following the MDTraj process.

Thank You
Sankar Maity