[gmx-users] RDF(PMF) and Umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 6 17:17:54 CET 2012

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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