GROMACS version: 2023
Dear all,
I have a very simple question. I want to open my trajectory file (md.xtc) using VMD, and I need to upload the necessary .gro file first. Here’s my question:
Which .gro file should be uploaded? the .gro file of the starting point of the production phase or the last point?
I also have another question. Is npt.gro exactly the starting point of the production phase?
Thank you so much
The .xtc file does not contain atom/residue names, so these are taken from the structure file (.gro or .pdb). In that regard, it doesn’t really matter which one you use, and you can remove the respective frame within VMD if you don’t want it to add to the trajectory; for example, if you do
vmd traj.xtc struct.gro
the command will work but the (potentially initial) .gro file will be added at the end of the trajectory, and it can mess up some time-series analyses.
Regarding the second question, it’s hard to answer exactly unless you share your full workflow, as there are no universal naming conventions for Gromacs. But if you run a job with e.g. -deffnm npt, then npt.gro will contain the last frame from that simulation part.
Thank you so much for your useful information