[gmx-users] Justin paper 2010 pulling
Justin Lemkul
jalemkul at vt.edu
Fri Sep 14 13:42:06 CEST 2018
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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>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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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>> 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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