[gmx-users] force/time application for pull

[Rakesh Mishra]

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, etc.
> > >
> > > -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> *
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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*