[gmx-users] Pulling ion - US

[Steven Neumann]

Would you also specify in each US window specific residue instead of
the whole protein?

Sreven

On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> 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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