[gmx-users] Justin paper 2010 pulling

Rakesh Mishra rockinbhu at gmail.com
Mon Sep 17 14:25:48 CEST 2018 

Agreed with this

"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."

The same I am saying that on  Pulling X, X will fell equal and opposite but
not Y and  Z.

Meaning ,
If 3' of one strand will Pull  along X then 3' (reference group , which is
not fixed )of complimentary strand  will move opposite along X . while Y
and  Z
those where no biasing force are applied, so Y and Z are  free to move in
random (any direction ).


Simple representation form your tutorial like.
In my thinking in this following protocol r_24 and r_12 will move
oppositely along X direction. But not Y and Z.

pull_ngroups               = 2
pull_ncoords               = 1
pull_group1_name        = r_24         ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name        = r_12          ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type          = umbrella      ; harmonic biasing force
pull_coord1_geometry   = distance      ; simple distance increase
pull_coord1_groups       = 1  2
pull_coord1_dim           = Y  N  N
pull_coord1_rate          = 0.005          ; 0.005 nm per ps = 5nm per 1 ns
pull_coord1_k              = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start         = yes           ; define initial COM distance > 0




On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>>>>>> 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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>>>>>>>>> or
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>
>>>>>>> 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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>>>>>>> * 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * 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
>>>
>>> ==================================================
>>>
>>> --
>>> 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
>
> * 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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