[gmx-users] Numbering for pbc_atom0

[Erik Marklund]

Nevermind. I figured it out I think. It was more of a problem with box size.

Erik

15 jun 2012 kl. 14.20 skrev 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
> 
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-----------------------------------------------
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

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