[gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

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 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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>
>

-- 
==================================================

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

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