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

[Shay Teaching]

Thanks for you prompt reply! Clear and to the point.
-Shay

On Tue, Jun 21, 2011 at 2:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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
>>
>>
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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