Gavin Melaugh wrote:
Hi Justin
Thanks for the reply. I wanted my "pulling" to be free in all
directions, that is in the liquid state with no defined reaction
coordinate i.e not along a specific axis. This is why I used geometry =
distance. Would you agree with this approach?
I suppose there is an argument that can be made for a more free approach such as
this one, but you're going to get the artifact you observed the instant your
pull group moves past a zero COM distance. Whether or not this is a significant
problem is something you'll have to determine.
-Justin
By free I mean. The absolute distance between the COG of the ref group
and that of the pull group.
Cheers
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Dear all
I have a query regarding umbrella sampling simulations that I have
carried out to study a dynamical process of a guest inserting into a
host. I always get get a wall tending off to infinity at or just before
the zero distance between the
two species.
The process I describe, for one system in particular, happens readily
and I have compared the PMF from a non constrained simulation (via the
RDF and reversible work theorem) and the same PMF from a set of
umbrella sampling
simulations. They agree quite well but in the non constrained simulation
I get a minimum practically at zero whereas for the umbrella sampling
the minimum is shifted and there is an infinite wall close to zero. This
wall is not present from the reversible work theorem. Why the infinite
wall? Why does the black histogram not centre around zero. Is this an
artefact of the umbrella technique? Please see attached the profile from
the umbrella sampling technique, and the corresponding histograms.
What's happening is the COM reference distance is changing signs, so
you get an artifact. The "distance" geometry is relatively inflexible
and is only suitable for straight pulls of continuously increasing or
continuously decreasing COM distance. You should try using the
"position" geometry instead. There are some notes that you may find
useful in my tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html
-Justin
Here is an excerpt from one of the umbrella mdp files.
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = tail
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 10000
pull_nstxout = 150
pull_nstfout = 150
Cheers
Gavin
------------------------------------------------------------------------
------------------------------------------------------------------------
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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