I am trying to construct the virtual site3 for my molecules, but I’m having issues understanding exactly what the indices corresponds to in the Figure 35 of GROMACS manual (the scheme with virtual sites constructions). I don’t know what do the factors a and b mean, and how to specify the a and b when the virtual site is on the opposite side as the figure drawn.
a and b are the coefficients multiplying the vectors, which are distance vectors between the constructing atoms. If you want the virtual site on the opposite side, as is usually the case, a and b should be negative.
For virtual_sites3, I need to first calculate the values of Wi, Wj, and Wk based on the coordinates between the particles and virtual atoms, and then calculate the values of a and b using Formula 284. Is my understanding correct?