Hi users, I am seeing some unexpected behavior for my COM pulling simulations. Errors arise from the COM and distance calculations and I reckon it can be fixed by increasing the box size and/or choosing good atoms as pbc_atomX in the mdp file. From the documentation it's not clear to me if it's molecule/group-local or global atom numbering that is used in this case. I've assumed global indices so far, but I'm not sure and I still see unexpected jumps in the dX after changing the pbc_atomX to what seems reasonable to me. Any input on this from users more experienced in COM pulling?
Best, ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
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