GROMACS version: 2025.0
GROMACS modification: No
Hello all,
I’m a doctoral student working on a membrane protein using large (~300,000 atom) systems. I’m having some issues with the post-simulation analysis of a particular residue.
I know that I’ve to define the particular areas of interest in the protein using the gmx select command. So when I’m calling the residues, it’s giving me a “group is empty response. Another caveat I found is that even though I’m referring to the .tpr file for the indexing, it’s sourcing the residue IDs from the original PDB residue numbers
For example:
Residue X has a GROMACS given number of 41, and in the PDB, which starts from 279, is 319. So, after gmx select when I’m calling the residue X as r 41, it’s giving me a response that > group is empty.
But when I’m typing > r 319, then it’s parsing the residue for indexing.
Now, the third problem is that in the PDB or GRO file, the chains are defined. It’s a repeat of 279 to 531 for all four monomers.
Thus, I’m lost while analysing the correct residues.
Any kind of guidance will be much appreciated.
Thanks in advance