[gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

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.

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 constant 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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-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

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