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

[Hoa Trinh]

Dear Mark & Justin,
Thank you very much. Hum, the name of variable nbonds is a bit misleading.

*Lan Hoa*

2017-10-26 6:10 GMT-05:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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>
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