Virtual sites precisions in manual description

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes (of the manual)

Dear all,

I’m trying to implement a third party tool, but I’m having issues understanding exactly what the indices corresponds to in the Figure 34 of GROMACS manual version 2020.3 (the scheme with virtual sites constructions). In particular, I would very much like to have the legend (i, j, k, l) for black dots on this figure.

Otherwise, a quick description here would totally make my day. But I believe this Figure 34 would be easier to understand with just a legend for black dots.

Thank you very much in advance,
Have a nice day

EDIT: Corrected figure number

2

Fig. 34?
3

Yes, this one !

4

Also I think I’m seeing this:

image
image1079×423 35.2 KB

Is there a chance the directions of the vectors could be inversed in the code versus in the manual ?
I’m using gromacs 2018.6.

5

The formulas for all virtual sites in the manual are correct. But indeed the sign or direction is wrong for site ‘3’. Since you usually want it to be on the side as drawn, it is probably better to add the minus signs, as you did, and not put the virtual site in between j and k.

6

Ok, thank you for your prompt answer