[gmx-users] Justin paper 2010 pulling

Rakesh Mishra rockinbhu at gmail.com
Mon Sep 17 10:52:25 CEST 2018 

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.


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
>>>>>>>> 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 .
>>>>>>>>
>>>>>>>> There is no such thing as a "standard" force cons
>>>>>>>> <https://maps.google.com/?q=no+such+thing+as+a+%22standard%
>>>>>>>> 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
>>>>>>>
>>>>>>> ==================================================
>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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-- 

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

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +918777496532*

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