[gmx-users] Pulling ion - US

[Steven Neumann]

On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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

Thank you Justin. That indeed helped.

Steven
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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