Thanks for the reply
I have understood how the Lennard Jones pointers are laid out in the
topology file and now I will try to write a code to do what I want.
On Thu, Jul 26, 2018 at 11:00 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> The topology files do not store the sigma values for each atom (or even the
> combined sigma for each atom pair). Is that the 'sigma" you're talking
> about?
>
> You can do what you want within ParmEd, but it'll take some work to do
> precisely what you want (and will require writing code and understanding
> how the Lennard-Jones pointers are laid out in the topology file).
>
> HTH,
> Jason
>
> On Wed, Jul 25, 2018 at 12:36 AM, Leena Aggarwal <leena.hrc.gmail.com>
> wrote:
>
> > Dear Amber Users
> >
> > I want to use coupling parameters (say 'a' and 'b') in the Kirkwood
> > charging formula to scale the Lennard Jones parameters (a* sigma) and
> > (b*charge) so, I want to multiply the constant 'a' with all sigma values
> in
> > the topology file.
> >
> > On Wed, Jul 25, 2018 at 4:58 AM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Tue, Jul 24, 2018, Leena Aggarwal wrote:
> > >
> > > >
> > > > Can we multiply the existing Lennard Jones parameters of the topology
> > > file
> > > > by a constant using parmed ??
> > >
> > > Changing epsilon will multiply an existing LJ term by the ratio of the
> > new
> > > to the old epsilon value. Maybe that will do what you want?
> > >
> > > ....dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 26 2018 - 22:00:03 PDT
