[gmx-users] pull_pbcatom1 and pull code in gromacs 4
chris.neale at utoronto.ca
Thu Oct 30 18:16:56 CET 2008
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
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?
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