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 <jalem...@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 <jalem...@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 <jalem...@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 <jalem...@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
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303 Engel Hall
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Blacksburg, VA 24061
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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
jalem...@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
jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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