[gmx-users] Regarding free energy calculation

[Rakesh Mishra]

Thanks Bratin ,

But I think I don't want this one. Can any one tell us
Which Amber force-field is best one for DNA simulation
in current days..

On Fri, Nov 1, 2019 at 3:26 PM Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
wrote:

> Hi
>    You can follow the link below
> http://www.mdtutorials.com/gmx/umbrella/index.html
>
> On Fri, Nov 1, 2019 at 10:40 AM Rakesh Mishra <rockinbhu at gmail.com> wrote:
>
> > Dear Justin
> >
> > If we have simple duplex of DNA initially and than we have separated
> > both the strand by constant velocity stretching. Hence now we have two
> > states, one is bound state in the initial phase ( both strands are binds
> > with each-other)
> > and other is unbound state ( both strands separated) in the final phase
> of
> > tine.
> > Now if we want to calculate the DElTA_G ( binding free energy ), than is
> > there
> > any way in GROMACS to obtain this or we need to take help from some other
> > mean.
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-- 

*With Best-Rakesh Kumar Mishra  (RA)*

*Dr. D. S. Kothari Fellow.School of Computational *
*& Integrative Sciences, JNU.*
*Phone n. +91 9473662491, +918777496532*