[gmx-users] Pulling ion - US
jalemkul at vt.edu
Mon Dec 10 15:11:32 CET 2012
On 12/10/12 9:01 AM, Steven Neumann wrote:
> Dear Gmx Users,
> I am pulling away cation from the protein glutamic acid residue with:
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = Protein
> pull_group1 = NA
> pull_rate1 = 0.01
> pull_k1 = 500 ; kJ mol^-1 nm^-2
> I tried different pulling rates and simulation time to pull it 3 nm
> away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so
> strong that the force reaches 600 kJ/mol/nm2 and they do not become
> separated - with position restraints protein looses its secondary
> structure and is draged by the ion - they do not become separated.
> Would you suggest constant force pulling in this case? Then I will
> extract initial coordinates for US windows. Can I use then US with
> harmonic potential in windows then and WHAM?
You can generate coordinates in any way you wish. I would think that,
regardless of the pull method, setting pull_group0 to the actual residue to
which the ion is coordinated would be significantly more effective than pulling
with respect to the entire protein, though it seems rather strange that the
dissociation of an ion would cause a protein to unfold. A stronger force
constant in pull_k1 may also help.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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