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
> >
> >
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--
Jason M. Swails
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Received on Thu Jul 26 2018 - 11:00:06 PDT
