[gmx-users] Numbering for pbc_atom0

Erik Marklund erikm at xray.bmc.uu.se
Fri Jun 15 14:20:28 CEST 2012

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?


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
erikm at xray.bmc.uu.se

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