[gmx-users] Regarding free energy calculation

[Alessandra Villa]

Hi,

You could try AMBER99 BSC1.
FF implementation could be found in
http://www.gromacs.org/Downloads_of_outdated_releases/User_contributions/Force_fields
(amber99bsc1.ff.tgz
<http://www.gromacs.org/@api/deki/files/260/=amber99bsc1.ff.tgz>)
Best regards
Alessandra <http://www.gromacs.org/@api/deki/files/260/=amber99bsc1.ff.tgz>
<http://www.gromacs.org/@api/deki/files/260/=amber99bsc1.ff.tgz>


On Wed, Nov 27, 2019 at 6:07 AM Rakesh Mishra <rockinbhu at gmail.com> wrote:

> 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*
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