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.
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
