[gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

While I have purely physics background.

But, In my thinking, there are hydrogen bonds (electrostatic attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01, 0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .  Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
not .




On Thu, Sep 6, 2018 at 5:31 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>
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-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

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