[gmx-users] force/time application for pull

Rakesh Mishra rockinbhu at gmail.com
Mon Aug 27 08:54:55 CEST 2018 

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 Mon, Aug 13, 2018 at 6:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
>
> On Mon, Aug 13, 2018, 13:42 Rakesh Mishra <rockinbhu at gmail.com> wrote:
>
> > Hello Mark,
> >
> > Thank for  your clarification. Gromacs pulling has simple protocol for
> > pulling
> > using umbrella sampling. Where one can only get f/t and x/t . here t is
> > linearly
> > increases for both cases of force and distance. That actually not full
> fill
> > the need of
> > experimental pulling.
> >
> >
> > On Mon, Aug 13, 2018 at 3:26 PM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > It's possible, but there is no code written for it.
> > >
> > > Mark
> > >
> > > On Mon, Aug 13, 2018, 12:47 Rakesh Mishra <rockinbhu at gmail.com> wrote:
> > >
> > > > Dear Justin.
> > > >
> > > > Thanks for your kind  advise.
> > > > But why don't it is not  possible to apply the constant force which
> > > should
> > > > increases linearly (at each instant of time delta)
> > > > like at
> > > > t1 -f1
> > > > t2-f2
> > > > .
> > > > .
> > > > tn-fn
> > > >
> > > > and corresponding to that force we get extension for each increment
> of
> > > > time in Gromacs. This is more relevant in order to map
> > > > experimental work of unzipping or axial pulling of nucleic acid like
> > > > DNA/RNA/protein.  Is it possible to build this protocol in Gromacs.
> > > >
> > > > On Thu, Aug 9, 2018 at 5:30 PM Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 8/9/18 6:37 AM, Rakesh Mishra wrote:
> > > > > > Dear all,
> > > > > >
> > > > > > Can anyone shed some light as ,Is it possible to apply force/time
> > for
> > > > > > pulling in gromacs. Means I want to pull my system in step wise .
> > eg.
> > > > > >    0 - t1     force applied f1
> > > > > >    t1+dt  to t2     force f2
> > > > > >    t2+dt  to t3     force f3
> > > > > >    .
> > > > > >    .
> > > > > >    .
> > > > > >    tn-1 +dt  to tn     force fn
> > > > > >   Is it possible.
> > > > >
> > > > > Not in a single run. You would have to run a simulation for
> interval
> > 0
> > > -
> > > > > dt, generate a new .tpr file for the time period of (t1+dt) - t2, e
> > <https://maps.google.com/?q=le+for+the+time+period+of+(t1%
> 2Bdt)+-+t2,+e&entry=gmail&source=g>
> > tc.
> > > > >
> > > > > -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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> > > > --
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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> *
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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*

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