[gmx-users] (no subject)

[Rakesh Mishra]

Dear  Mark,

I think things are not under solution.

Please tell me if there is  dsDNA of chain A (12 bp)
and  complimentary strand B(12 bp)  like

chain A-   3' - 5'
chain B-   5' - 3'
I am pulling   5' end  of strand  A and made 5' of B as a reference group
along the helical direction under constant velocity pulling. And both the
chains are free ( no restraint) ,
under this situation will the 5' of chain B (act as reference group) feel
the equal and opposite force like 5' end of chain A where pulling is
applied .
Due to this equal and opposite force both the strand will move opposite to
each other or not .



On Mon, Sep 3, 2018 at 10:00 AM, Rakesh Mishra <rockinbhu at gmail.com> wrote:

> Hi Mark
>
> Did you get the point or  not .
> Hoping your  response
>
> On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra <rockinbhu at gmail.com>
> wrote:
>
>>
>> *Please remember (its your  query to me )*
>> Hi,
>>
>> Can you please share a link to something that indicates why this would be
>> a
>> good tool for modeling such experimental pulling scenarios? Making the
>> case
>> for implementing such a feature would benefit from that.
>>
>> Mark
>> > <https://maps.google.com/?q=le+for+the+time+period+of+(t1%2B
>> dt)+-+t2,+e&entry=gmail&source=g
>> <https://maps.google.com/?q=le+for+the+time+period+of+%28t1%2Bdt%29+-+t2,+e&entry=gmail&source=g>
>> >
>>
>>
>>
>> *This is our response *
>>
>>
>> Dear Mark,
>>
>> There are several experiments have been done for protein and DNA
>> unfolding.
>> Thy  became pioneer in this field.  That is why force should apply and
>> corresponding reaction
>> coordinates are measured . Here Gromacs login do not allow to upload
>> larger data.
>> But I can mention some paper address . If get time Please go through
>> these papers .
>>
>> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
>> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>>
>> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
>> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>>
>> That is  why I  asked about force-extension protocol.  In Umbrella
>> sampling distance is increases linearly with the time and corresponding
>> force experienced by the system writes .
>>
>> We still don't no that force/time which writes in .xvg file corresponds
>> which formula like f= k(vt-x) or something else.
>> There are other lot experiments regarding measurement of stability of the
>> DNA and protein under f/x curve.
>> One can see some theory paper also to see f/x like.
>>
>> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>>
>>
>>
>>
>> Note- According to Justin one  can write that protocol. If suppose we
>> write that protocol, then how  to apply in gromacs.
>>
>> There are only input .mdp files. We didn't know  where to built the force
>> subroutine in .ff (force field ) directory. or somewhere else.
>>
>>
>> Hoping for  response.
>>
>>
>>
>>
>>
>>
>> On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra <rockinbhu at gmail.com>
>> wrote:
>>
>>> Dear  mark
>>> I had already discussed regarding force/extension protocol.
>>> But I didn't get any response from your side. I dont have
>>> idea to upload some pictures.
>>>
>>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> The list cannot accept attachments. Upload to a file sharing service and
>>>> share a link. We will likely need more background information also.
>>>>
>>>> Mark
>>>>
>>>> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra <rockinbhu at gmail.com> wrote:
>>>>
>>>> > Hi every body
>>>> > can any one  explain what is the mean of this graph
>>>> > obtained from gromacs  constant velocity pulling of dsDNA
>>>> > along the helical direction. (force.xvg). Basically sudden drop of
>>>> force
>>>> > represents what ?
>>>> > --
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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*
>>>
>>
>>
>>
>> --
>>
>> *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*
>>
>
>
>
> --
>
> *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*
>



-- 

*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*