[gmx-users] (no subject)
rockinbhu at gmail.com
Fri Aug 31 14:48:00 CEST 2018
*Please remember (its your query to me )*
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.
*This is our response *
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
coordinates are measured . Here Gromacs login do not allow to upload larger
But I can mention some paper address . If get time Please go through these
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>
>> The list cannot accept attachments. Upload to a file sharing service and
>> share a link. We will likely need more background information also.
>> 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*
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