[gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

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

==================================================