[gmx-users] another pull-code question

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 1 19:34:03 CEST 2010

Gavin Melaugh wrote:
> Hi All
> I am using COM pulling to pull two molecules together in order to
> calculate the potential of mean force and the pulling is fine. I am
> using pull = umbrella for the pulling as I am following
>  the tutorial on the website. If I use pull = constraint does this still
> pull the molecules together, and if so do you still then need to 
> perform umbrella sampling on the configurations generated? I am a little
> confused  as I don't understand how the molecules pull together if they
> are constrained.

For plain SMD, you can use any of the pull methods.  In the tutorial I wrote, I 
explain why I used "pull = umbrella" during SMD.  Umbrella sampling is a 
separate procedure, which can be done after SMD.  If you want a free energy 
along the reaction coordinate, there are several methods for doing this, among 
which is umbrella sampling.


> Many Thanks
> 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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