[gmx-users] Pull code

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> Thanks. If I use the pull_geometry = direction I would go for the
> following jus t to pull the molecules together in the z direction.
> 
> pull        = umbrella
> pull_geometry = direction
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = cage_1
> pull_group1 = cage_2
> pull_vec1 = 0.0 0.0 -1.0
> pull_rate1 = 0.01
> pull_k1 = 1000
> 
> 
> Does this seem reasonable? Also in the pull_rate what is meant by the

Probably.  Try it.

> 'rate of change of the reference position'? (Is it the position of the
> reference group, if so what if I don't want it to change?)
> 

It is the rate of change of the reference position, which is the position at the 
outset of the simulation.  Your objective is to pull your two species together, 
right?  I don't see why you wouldn't want it to change.  You're not changing 
anything about pull_group0 (your reference group), since you aren't setting 
pull_rate0.  Everything is applied to pull_group1 (hence _rate1, _k1, etc).

-Justin

> Cheers
> 
> 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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