Dear Users,
I am performing umbrella sampling simulations of the ring closure of
DNA minicircles. The problem with pull_geometry=distance is that the
end-to-end distance used as general coordinate becomes at some point
larger than half the box size. The distance to the closest image is
used in the histogram generation and WHAM procedure what is of course
wrong. To avoid this problem I tried pull_geometry=direction_periodic
with pull_vec1 taken as the vector between both ends of the DNA
fragment and one end frozen but this set-up does not seem to work
properly. Does anyone have a solution? Is there a possibility to
implement a pull_geometry=distance_periodic in a next version of
gromacs?
Thank you for helping!
Below are the relevant options used for umbrella sampling:
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
pull_group0 = start
pull_group1 = end
pull_k1 = 100
pull = umbrella
pull_geometry = direction_periodic
pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
pull_group0 = start
pull_group1 = end
pull_vec1=-0.4160005.3 -0.2650005.3 -2.4920005.3
pull_k1 = 100
freezegrps = start
freezedim = Y Y Y
--
Aymeric Naômé
Ph. D. Student
UCPTS Division
University of Namur
61 Rue de Bruxelles
5000 Namur
BELGIUM
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
