[gmx-users] Pull code

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi all
> 
> I am commencing the initial stages for he calculation of potential of
> mean force of bringing together two cage molecules. I am following the
> tutorial in such an exercise at
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
> In contrast to the tutorial I want to bring the two molecules together
> along the z axis. I have generated an initial configuration in which the
> COMs of the two molecules are 5.07 nm apart.
> In the tutorial to separate a substrate from a protein you use the
> following parameters in the mdp file.
> 
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance
> pull_dim        = N N Y
> pull_start      = yes           ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Chain_B
> pull_group1     = Chain_A
> pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per n
> pull_k1         = 1000          ; kJ mol^-1 nm^-
> 
> 
> How should I alter this to pull the molecules together along the z axis?
> I would've thought the following but I'm not too sure
> 
> pull        = umbrella
> pull_geometry = distance
> pull_dim = N N Y
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = cage_1
> pull_group1 = cage_2
> pull_rate1 = -0.01
> pull_k1 = 1000
> 
> 
> Obviously I have to play with the values, but it is the sign that I'm
> interested in.
> 

Have you tried it?  I think it should do what you want.  Otherwise, it is 
probably easier to use "pull_geometry = direction" and specify the actual vector 
along which to pull.  The tutorial is only really useful from a conceptual 
standpoint, and for a system in which pulling is applied in only one direction 
to cause a positive displacement.

-Justin

> Many Thanks
> 
> Gavin

-- 
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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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