Hi Jason
You wrote that "radius = 2^(1/6)*sigma". But when I cross check the value
for water oxygen we found that the given value is actually Rmin/2.
Rmin=2^(1/6)*sigma
Does the outcome is Rmin or Rmin/2?
Regards
On Fri, Sep 5, 2014 at 7:29 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Sep 5, 2014 at 9:46 AM, Uday Midya <umidya.iitkgp.gmail.com>
> wrote:
>
> > Hi All
> > I require the numerical value of *epsilon* and *sigma *for each atom in
> my
> > system. I find in amber topology file that their product is given in the
> > *Aij* and *Bij* form for each pair of atom type. Can any one suggest me
> how
> > to get the *sigma *and* epsilon*?
> >
>
> ParmEd will print them out for you. Just use the "printDetails :*"
> command to print the details on all of the atoms in the system. For
> example:
>
> parmed.py -p prmtop << EOF
> printDetails :*
> EOF
>
> It will list (among many other properties), the LJ radius and LJ depth.
> The sigma parameter is related to the radius by "radius = 2^(1/6)*sigma"
> and the well depth is epsilon.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
Uday Sankar Midya
IIT Kharagpur
West Bengal
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Received on Fri Sep 05 2014 - 10:30:02 PDT
