[gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial)

[Justin A. Lemkul]

Shay Teaching wrote:
> Dear Gromacs Users,
> 
> I've done Justin's tutorial regarding PMF/umbrella sampling and now, 
> when approaching my own system I have a couple of questions.
> (Link to the tutorial here: 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html 
> )
> 
> My system is comprise of a transport protein (embedded in membrane) and 
> a ligand. The system is positions so that Z axis is the axis on which 
> I've made PMF windows.
> The next step on this is to run these windows separately and I didn't 
> quite understand why in step-6 of the tutorial it specifies to still use 
> pull_dim = N N Y and pull_rate1 = 0.0.
> 
> As far as I understood, during the production run we want to sample the 
> Z position. Shouldn't then it use pull_dim = Y Y N ?

No, that would confine the pulled group to the x-y plane, but allow it to move 
freely in z.

> And what does it mean to the system when we set pull_rate1 = 0.0 ?

The harmonic restraint is applied to pull_group1 such that there is no net 
change in position.

> Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it 
> restrains pull_group0 on the Z-axis?
> 

Not pull_group0 (which is the reference group), but pull_group1.  Otherwise, yes.

-Justin

> This came a bit longish,
> Thanks in advance,
> 
> -Shay
> 
> P.S.
> Using Gromacs 4.0.7
> 
> 
> 

-- 
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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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