GROMACS version: 2020.3
GROMACS modification: No
How do I look at the atoms selected with gmx make_ndx in a program like Chimera? I want to make sure I’ve selected the right atoms. Thanks in advance for your help with this! It is greatly appreciated.
Provide index file to trjconv tool to dump desired coordinates
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If you don’t have a trajectory yet you can also do it with editconf or select.
Thank you so much for these suggestions!
I was able to figure out why my index groups didn’t make sense: It had numbered the residues in the multi-chain structure in a different way than they were numbered originally so I wasn’t selecting what I thought I was selecting. Ultimately I ended up doing the analysis on the MD trajectory in Chimera