[gmx-users] Calculated bonded interactions - number of bonds- bondfree.c
jalemkul at vt.edu
Thu Oct 26 13:11:03 CEST 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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