# [gmx-users] Justin paper 2010 pulling

Justin Lemkul jalemkul at vt.edu
Mon Sep 17 13:48:37 CEST 2018

On 9/17/18 4:52 AM, Rakesh Mishra wrote:
> Agreed.
>
> But, I could not solve.
>   So Justin, If I pull 3' end of one strand of DNA by taking as
> 3' end of the complimentary strand as a reference group (Note that
> I have not fixed or not made it immobile ) then according to the theory of
> newtons third law reference group (which is not immobile or not fixed )
> will get
> same equal and opposite pull and will move in the opposite direction.
> am I correct.

You set two groups that define a vector along which a biasing potential
is applied. The net displacement of either of those groups (or any other
atoms in the system) is a function of the total force acting on all of
the atoms. Newtonian mechanics always apply, but it's not as simple as
"pull on X, and Y moves." Your system evolves under the influence of the
biasing force.

Your results are probably somewhat confounded by the fact that you're
pulling along a vector that is oblique to both the helical axis and the
hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA,
so judicious choice of pulling vector is critical.

-Justin

>
> On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 9/14/18 3:14 AM, Rakesh Mishra wrote:
>>
>>> Dear Dr. Justin,
>>>
>>> Of course I agree with your points. There is no point to not believe on
>>> you,
>>> that's why we are discussing and thanks for your comment.
>>> I raised the question because I observed the problem .
>>> And it was matter of just common sense for me that
>>> why the change of saving frequency is affecting the much difference
>>> in the maximum value of force curve in pulling along the axial direction.
>>>
>>> Let me clear again, I say Input parameters of the pull.mdp files are same
>>> for both the simulation.
>>> Only difference is the different saving frequency of position and energy
>>> coordinates.
>>> Please see below two cases
>>>
>>> Case -A
>>>
>>>     simulation of same system with same input parameter during pulling
>>> 1  nstxtcout    = 2000       ; every 4 ps
>>>       nstenergy    = 5000
>>>
>>> 2  nstxtcout    = 2000       ; every 4 ps
>>>       nstenergy    = 2000
>>>
>>>      (output files, pullf1.xvg, and pullf2.xvg are different very much
>>> w.r.t
>>> peak value of force )
>>>       Same thing happening also in the following below case, please see
>>> this.
>>>
>>> Case B.
>>>
>>> 1  nstxtcout    = 2000       ; every 4 ps
>>>       nstenergy   = 5000
>>>
>>> 2-  nstxtcout    = 1000       ; every 4 ps
>>>        nstenergy   = 5000
>>>
>>> Because, now this gromacs discussion user platform do not allow to upload
>>> any other data (eg, plot, pdf file etc) otherwise I can upload the plot.
>>>
>> You can always upload images to file-sharing services and provide links.
>>
>> But first, watch the trajectories and see how they're behaving. The
>> systems are likely just doing somewhat different things, as I said before.
>> There is no reason to expect even the exact same .tpr file to produce the
>> exact same output (binary identical), for reasons stated here:
>> http://www.gromacs.org/Documentation/Terminology/Reproducibility
>>
>> Again, I emphasize that output control has no impact on the computation of
>> forces or anything to do with the pull code. This cannot be the reason for
>> differences in trajectories.
>>
>> -Justin
>>
>> On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>> On 9/13/18 1:20 AM, Rakesh Mishra wrote:
>>>>
>>>> I do not believe .
>>>>> Because if I run multiple simulation of pulling with the same system and
>>>>> with the
>>>>> same inputs then almost we are getting similar force/time curve.
>>>>> While we are getting different curve if we are saving position
>>>>> coordinates
>>>>> or energy
>>>>> coordinates with different frequency.
>>>>>
>>>>> There is no aspect of the code in which the computation of forces
>>>> depends
>>>> on output frequency. You're welcome to disbelieve me, but you're clearly
>>>> just getting different simulation outcomes from different inputs, or
>>>> there's something else that differs that you haven't realized or haven't
>>>> told us.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>> On 9/12/18 8:42 AM, Rakesh Mishra wrote:
>>>>>> Dear Justin
>>>>>>
>>>>>>> It is totally surprised for me.
>>>>>>>      I am pulling the same system of bdna
>>>>>>> with the same constant velocity (0.005nm/ps).
>>>>>>>
>>>>>>> Case 1
>>>>>>> let for first case, When I am saving position coordinate (nstxtc ) in
>>>>>>> the
>>>>>>> interval of 4ps
>>>>>>> and saving energy coordinate in the interval of 4ps.
>>>>>>>
>>>>>>> Case 2
>>>>>>> In the second case of pulling of the same system with the same
>>>>>>> velocity,
>>>>>>> we
>>>>>>> save position
>>>>>>> coordinate in the interval of 4ps but we save energy coordinate in the
>>>>>>> interval of  10ps.
>>>>>>>
>>>>>>> Now in the output file of force.xvg for both case qualitative
>>>>>>> behaviour
>>>>>>> of
>>>>>>> diagram is same but
>>>>>>> Peak of the forces are much differ.  Why this saving frequency is
>>>>>>> affecting
>>>>>>> the peak value. While
>>>>>>> it is just saving the coordinates.
>>>>>>>
>>>>>>> We also found that, if we save energy coordinate with the same
>>>>>>> frequency
>>>>>>> and position
>>>>>>> coordinate with different frequency then, again peak value of forces
>>>>>>> are
>>>>>>> different.
>>>>>>> Which should not. Why it is happening. Can you clarify please.
>>>>>>>
>>>>>>> Your results have nothing to do with the save frequency. The output in
>>>>>>>
>>>>>> pullf.xvg is specified by pull-nstfout, not any of the others. You have
>>>>>> different simulations that behave differently, because there are
>>>>>> elements
>>>>>> of randomness in any MD simulation. Pulling is a non-equilibrium
>>>>>> process;
>>>>>> you may have to run several times with different pull vectors to find
>>>>>> the
>>>>>> minimum-energy path.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>>
>>>>>>> On 9/6/18 2:29 AM, Rakesh Mishra wrote:
>>>>>>>
>>>>>>>> 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
>>>>>>>>> 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 .
>>>>>>>>>
>>>>>>>>> There is no such thing as a "standard" force cons
>>>>>>>>> 22+force+cons&entry=gmail&source=g>tant
>>>>>>>>> for pulling.
>>>>>>>>>
>>>>>>>>> -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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>>>>>>
>>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support
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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

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