[gmx-users] Numbering for pbc_atom0

[Erik Marklund]

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
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120615/d8e364ed/attachment.html>