[gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/5/18 1:50 AM, Rakesh Mishra wrote:
> So that means
>
> It is may be due to the  difference in the type of interaction.
>
> and I can not understand your this statement "you have to contend with
> forces principally acting perpendicular to the direction of the bias"
>

Well, what interactions act along the plane perpendicular to the helix 
axis of a duplex DNA or RNA?

-Justin

>
> On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 9/4/18 11:44 AM, Rakesh Mishra wrote:
>>
>>> Dear Justin,
>>>
>>> Seriously I want to remove my confusion.
>>> I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
>>> Where you have studied stability of Alzheimer. I don't want to ask about
>>> umbrella sampling used for the calculation of PMF.
>>>
>>> But , before the calculation of PMF , you
>>> have obtained simple dissociation using your  pulling protocol of gromacs
>>> with constant velocity simulation at three different velocities.  I am
>>> surprised that you have followed the obvious protocol
>>> of minimization the nvt the npt and then 100ns md production. then you
>>> took
>>> final structure of 100ns and made new box for pulling  and followed the
>>> same minimisation and npt for short time. After this you did pulling along
>>> only one direction (one reaction coordinate) .
>>>
>>> I am surprised that how such a smooth force/time data you have obtained
>>> for
>>> all the velocities (0.01,0.001,0.005) . I am asking because for my simple
>>> 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed
>>> one end (say 5') of first strand and pulling opposite end (5') of second
>>> strand along the helical direction of the system. Here, I am getting
>>> force/time (in the .xvg ) data which is qualitatively similar behaviour
>>> like yours i.e.  initially increasing then reach to maximum and then
>>> decreasing almost becomes to zero value. But , In mine case during initial
>>> time of pulling force is also negative as well large fluctuation of force
>>> .
>>> But not such a smooth Variation of force/time like your in this paper. In
>>> your case, force is increasing like linearly in the initial and reaches
>>> the
>>> maximum and then start to decrease.  There is no problem to
>>> clarify the peak of force (maximum force) in your pulling (above mentioned
>>> paper). While in our case its very difficult to clarify the peak force due
>>> to large fluctuation in value.
>>> Can you please tell me something about the reason. Its smoothness is now
>>> became headache for my calculation in all the case of pulling.
>>>
>> There is no reason to think that your outcome and mine should look
>> anything alike. Pulling apart two proteins that interact in the way the
>> peptides do in a protofibril is much simpler than the intertwined nature of
>> a DNA or RNA duplex. If you pull along the helix axis, you have to contend
>> with forces principally acting perpendicular to the direction of the bias,
>> as well as the fact that the strands have to slide past one another,
>> requiring major distortion of the helix and/or frictional forces due to the
>> individual strands unwinding from one another.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================