[gmx-users] Re: gmx-users Digest, Vol 41, Issue 5: interaction lists in idef.h (wnoid at hec.utah.edu)

[Gerrit Groenhof]

>    8. interaction lists in idef.h (wnoid at hec.utah.edu)
>
>   

Dear Will,

Have a look at 
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/gromacs_I.pdf

In idef there is the ilist array, with an element for each of the F_NRE 
interaction types.

THis list is an 1D array of 1D arrays. Depending on how many atoms are 
involved in a specific interaction (say n), these arrays are multiples 
of n+1, where the first element is an index into an iparams and ifunc 
array. The next elements are the actual atomnumbers in the simulations 
involved in this interactions. The ifunc contains the function, the 
iparams the parameter for that functions.

So if you want to have all the angles: loop though the ilist[F_ANGLE] in 
steps of 4 (see sheet 6) to get all the atoms triples and their 
interaction function (the same for all) and parameters (differnet for 
different atoms combinations).

Hope this will help you a bit further,

Gerrit