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.
-Justin
Many Thanks
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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