Can anyone help me with how to reimage your protein after simulations?

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Zhaoxi Sun

There is a flag named '-pbc' in trjconv of gmx_mpi. Often, the -pbc whole or -pbc mol could work, but this is not guranteed.

Rahul Sahu

Purva Khodke

bring your protein to the center of the box using -center -pb mol flag. After that applying -fit rot+trans will fix the protein with the reference structure while the remaining part will translate and rotate accordingly.

Thank you Rahul Sahu Zhaoxi Sun