[gmx-users] (no subject)

[Rakesh Mishra]

*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*