GROMACS version: 2025.1
GROMACS modification: Yes/No
Hi Everyone!
I was using gmx mindist to check if a (large) number of simulations were done using an adequate box size. I was havinga. hard time to fix PBC and run the mindist on the trajectories when it comes to multichain proteins. Does anyone have any kind of experience with similar problems?
I was trying to fix PBC with the gmx, “trjconv”, “-s”, str(tpr),“-f”, str(xtc),c"-o", str(mol_xtc), “-pbc”, “whole”, and also running gmx, “trjconv” “-s”, str(dummy_tpr) “-f”, str(mol_xtc) “-o”, str(tmp_xtc) “-pbc”, “whole” “-center”, but it does not seem to see my protein complexes as a whole and will put cut the PBC at a wrong spot esenntially making mindist calculate the distance between the complexed proteins instead of the distance between complexes.
Thank you all for any help!