[gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

[Justin Lemkul]

On 10/26/17 1:56 AM, Hoa Trinh wrote:
> Hi all,
> I am trying to look into the source code of Gromacs 5.0.7 to see how
> Gromacs calculate bonded interactions. For example, to calculate bond
> interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
> real bonds(int nbonds, ...)
> {
>    ....
>    for (i = 0; (i < nbonds); )
>      {
>          type = forceatoms[i++];
>          ai   = forceatoms[i++];
>          aj   = forceatoms[i++];
> ....
> }
> Is "nbonds" the total number of bond interactions? In my topology file, I
> have 126 pairs in the [ bonds ] section. However, when I printf the
> variable nbonds, it appears to be 378. I have no idea why. Can anyone
> please help me to explain what is nbonds?

378 = 126 * 3

nbonds here indicates the size of the array, which holds (type, ai, aj) 
for each bond in the system.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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