[gmx-users] (no subject)

[Rakesh Mishra]

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*