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
--
========================================
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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