[gmx-users] Justin paper 2010 pulling
Rakesh Mishra
rockinbhu at gmail.com
Fri Sep 14 09:14:58 CEST 2018
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.
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
>>>
>>> ==================================================
>>>
>>> --
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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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