[gmx-users] CMAP format on GROMACS

[Justin Lemkul]

On 1/8/20 10:25 AM, Marcelo Depólo wrote:
> Thanks for your input, Justin. Helpful as always.
>
>
> I am assuming the array is formatted to vary phi as a function of psi
> i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and
> again but for phi = -165.
>
> I am also assuming that, since it is a 24x24 matrix, values will start in
> phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix
> would lead to end in phi=180,psi=180, but since they -180 and 180 are
> equivalent, maybe GROMACS already do this workaround?

+/- 180 are understood to be equivalent.

> The last question: are those values in kJ/mol?

Yes. GROMACS always uses SI units.

-Justin

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Justin A. Lemkul, Ph.D.
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