[gmx-users] Justin paper 2010 pulling
Justin Lemkul
jalemkul at vt.edu
Mon Sep 17 15:12:22 CEST 2018
On 9/17/18 8:50 AM, Rakesh Mishra wrote:
> 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 ).
If the helix rotates, your application of a bias only along x becomes
invalid or will do something you don't want.
> 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.
Again, this is just a natural outcome of the biasing force being
interpolated onto the affected atoms.
-Justin
>
> 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
>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>> ==================================================
>>>>>>>>>>>>
>>>>>>>>>>>> --
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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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>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> 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
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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
>>
>> ==================================================
>>
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>> 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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