[gmx-users] force/time application for pull

[Mark Abraham]

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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