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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Received on Fri Sep 05 2014 - 07:00:03 PDT
