[gmx-users] pull_pbcatom1 and pull code in gromacs 4

Berk Hess gmx3 at hotmail.com
Fri Oct 31 09:58:17 CET 2008


This issue is caused by the use of domain decomposition instead
particle decomposition.

However, this does not have much to do with the "nojump" behavior
you are talking about.
The pbcatom is only used for determining the COM of one group.
The distance between COM's was always done with full pbc,
which means that the vector between the two closest images is used.

Note that the choice of pbcatom only has an effect for groups with
and x, y or z size that is more than half the box length.
(and it does not at all affect how the distance between groups
is determined)


> Date: Thu, 30 Oct 2008 13:16:56 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull_pbcatom1 and pull code in gromacs 4
> Hello,
> The pull-code .mdp option pull_pbcatom1 is defined in the online manual as:
> "The reference atom for the treatment of periodic boundary conditions 
> For determining the COM, all atoms are put at their periodic image which 
> is closest to pull_pbcatom1. A value of 0 means that the middle atom 
> (number wise) is used."
> I suppose that this is necessary since mdrun now writes broken 
> molecules. However, this is suboptimal for replica exchange umbrella 
> sampling (pull = umbrella, pull_geometry = distance) in which one does 
> not necessarily want to utilize different periodic images of pull_group0 
> and pull_group1.
> a) Perhaps I don't understand. Is it possible that although a particular 
> image of each pulled group is chosen, the pulling is actually still done 
> along the vector between the closest two images?
> b) If not, is there a simple code modification to utilize a pbc=nojump 
> type definition here during dynamics?
> Thanks,
> Chris.
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