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

[Shay Teaching]

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 ?
And what does it mean to the system when we set pull_rate1 = 0.0 ?
Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains
pull_group0 on the Z-axis?

This came a bit longish,
Thanks in advance,

-Shay

P.S.
Using Gromacs 4.0.7
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