[gmx-users] force/time application for pull

[Rakesh Mishra]

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 

*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*