[gmx-developers] Pull to COM of molecules

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Apr 16 16:03:36 CEST 2009

I can't comment from a code level, but I have been doing this recently  
in my simulations. It was key for me to set pull_pbcatom0 to be an  
atom that is generally in the center of the reference group. Then  
either 1) the box must be big enough that the other atoms in that  
group are always placed in the same cluster (not necessarily the same  
unit cell), or 2) the run must be completed in segments and some  
script should exist to rationally choose an optimal central  
pull_pbcatom0 to start the next short mdrun segment.

Both of these are a little frustrating and myself and one other user  
are currently getting some strange results in combination with the  
free energy code, even with large boxes, but it certainly appears to  
be working as expected.

I have an item on the wiki wish list that outlines how the situation  
could be dramatically improved here, and I have been in contact with a  
programmer to get this modification made, although that will take some  


Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> Hi,
> is it possible to pull somehting to the center of mass of a group of
> molecules? My guess (and preliminary experience) seems to say that this
> is not possible due to the periodic boundary conditions. Does the
> virtual site construction for center of mass solve this?
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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