[gmx-users] force/time application for pull

[Rakesh Mishra]

So, Dear Justin and Mark

Basically in Gromacs pulling using umbrella sampling.  Force corresponding
to the distance increment
during constant velocity pulling becomes like.
F= k(vt-x)
k=spring constant
v= constant velocity
t=time
x= distance between pulled group and reference group.

The force file (f/t) which we get  corresponds  that the force that feels
by system when distance increase.
And the sudden drop of force nearly zero corresponds that the strands (here
the case of dsDNA/siRNA)
are ruptured or melted (like force induced melting).

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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> > > > *With Best-Rakesh Kumar Mishra*
> > > > *  (RA)CSD  SINP Kolkata, India*
> > > >
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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*