[gmx-users] CMAP format on GROMCACS

[Justin Lemkul]

On 1/6/20 4:46 PM, Marcelo Depólo wrote:
> Hi everybody! Happy new year! =)
>
>
> I would like to understand a little bit better the CMAP format of
> charmm27.ff within GROMACS. I've looked up in the manual but found little
> information.
>
> I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a
> arbitrary identification number (e.g. 1) and the grid size (e.g. 24x24).
> But the following grid values are lines with just 10 values each, ended
> with a "\", instead of a 24 columns- 24 lines matrix.
>
> How are those values of CMAP formatted  in GMX? Does GMX automatically
> transform those values in a matrix and, if so, can I consider that its
> "y-axis" would be PSI and "x-axis" would be PHI?

The \ are line continuation characters, so GROMACS is reading a 24x24 
matrix in a single array of values.

The values are written for all values of phi at a given value of psi, 
i.e. writing each row of the matrix, starting from phi = -180, psi = 
-180 until phi = 180, psi = 180.

-Justin

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Justin A. Lemkul, Ph.D.
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