Hello, I use the TRR file to observe the trajectory of molecular motion, appeared in the picture of this phenomenon, excuse me this phenomenon is normal? If not normal, how should I improve it? Thank you
Hi,
You need to make the molecules whole (so that they are not broken across the periodic boundaries), then your molecular visualization will not show those long lines.
Best,
Carsten
Hi,
Thank you for your guidance. I’m a novice, so I’m still not sure how to make the molecule whole. Could you tell me a bit more about the steps? Thank you very much.
Hi,
you can do it with the -pbc option to gmx trjconv. Please have a look at the documentation for the options that best suit your needs:
https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html#gmx-trjconv
Best,
Carsten
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I solved it, thank you very much! I wish you all the Best ~