[gmx-users] force/time application for pull

[Mark Abraham]

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*
> > >
> > > *E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
> > >
> > > *Phone n. +91 9473662491, +918777496532*
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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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