# [gmx-users] Justin paper 2010 pulling

Rakesh Mishra rockinbhu at gmail.com
Mon Sep 17 14:57:17 CEST 2018

```In my above protocol,

What I found that, my system (12 dsDNA) placed with their helical axis is
along the X  axis (in VMD we checked ).
When I am applying pulling on r_12  ( with  pull_coord1_dim     = Y  N  N
). Keeping r_24 as a reference group (not fixed).
Distance between both group is increasing along X axis. In VMD it is
clearly showing that both the group are
moving in opposite direction along the helix ( X axis) direction. Which is
showing that r_24 is feeling equal pulling like r_12 (on which pulling is
applied)
in the opposite direction of biasing vector. i. e.  r_24 is moving in  -X
direction and r_12 is moving in +X direction.

On Mon, Sep 17, 2018 at 6:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/17/18 8:25 AM, Rakesh Mishra wrote:
>
>> 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."
>>
>
> Perhaps my nomenclature was bad here - X and Y are not Cartesian
> directions, they are the groups that you're specifying in the .mdp file
> that define the vector of the pulling force.
>
> The same I am saying that on  Pulling X, X will fell equal and opposite but
>> not Y and  Z.
>>
>
> Correct.
>
> 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.
>>
>
> The problem here is the the groups *will not* necessarily "move oppositely
> along X." Your biasing force causes a net increase in the length of the
> vector connecting r_12 and r_24. That's it. Perhaps that means one group
> moves and the other oscillates in place. Maybe they do, in fact, move in
> different directions. The net motion of any group depends on all of the
> forces in the system. Maybe your biasing potential causes a local helical
> unwinding, allowing water to enter in between the bases or the hydrogen
> bonding structure changes, which then causes different diffusion in any
> dimension. But the biasing force only ever applies along X.
>
> -Justin
>
>
> 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
>>>>>> 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
>>>>>>
>>>>> 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
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> 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
>>>>>>> /Mailing_Lists/GMX-Users_List before posting
>>>>>>> !
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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
>>>>> /Mailing_Lists/GMX-Users_List before posting!
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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
>
> * 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*
```