[gmx-developers] center of mass bug with pulling reference group

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Apr 27 13:50:38 CEST 2010

Dear Berk:

you and I discussed this a while ago and I proposed the following  
solution, which I still think is valid. The discussion at that point  
was in regard to pulling with micelles, and you suggested an  
alternative cosine-based method, but I think that the principles are  
the same:

Every N steps, and separately for each pull and reference group, loop  
through all atoms in the group and, assuming that this atom is the  
pull_pbcatom, determine the RMSD from that atom to each other atom in  
the same group. There must then be one or many "central" atoms that  
return the same minimum RMSD value. One of these "central" atoms is  
then set as the new dynamic pull_pbcatom. In order to allow N>>1, one  
chooses the one of these "central" atoms whose position is closest to  
the center of mass of the entire group after it is put into it's  
appropriate box based on the selected new pull_pbcatom for that group.

The only downside that I can see with this method is that it might  
offer a false sense of security in that it can fail, although only in  
cases where a static intelligently selected pull_pbcatom would also  
fail. Although it seems to me that this method would be more robust:  
e.g. with the current static pull_pbcmol, when pull_pbcmol is selected  
as the distal carbon of a lipid acyl chain, then if the box is small  
enough that reference atom can fluctuate near the headgroups at the  
same time as a different lipid fluctuates up along the bilayer normal,  
causing a selection of pbc that is other than desired.


Quoting Berk Hess <hess at cbr.su.se>:

> Jochen Hub wrote:
>>>> Thanks a lot Berk,
>>>> Jochen
>>> In x-y it should not matter.
>>> But what might matter is that distances of atoms in the bilayer to the
>>> pbc atom are larger
>>> than half the box length, if the pbc atom is in a head group instead of
>>> in the middle of the bilayer.
>> Aaahh, not again the bloody pbc_atom... :(( Arrrg, I had this problem
>> already 2 years ago, but I forgot, hmpf.  We fixed the script and now
>> things are all right. So all my apologies for waisting your time. :)
>> And thanks a lot for your help!
>> Best wishes,
>> Jochen
> This is a nasty issue that we should really try to automate.
> The problem is that I am not sure if there is a unique, good solution
> that would work in 99% of the cases.
> Berk
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