GROMACS version:2021.4
GROMACS modification: No
Dear all,
I’m trying to map the AA model to the CG model, but I’m having issues understanding exactly the calculated weights in 288. When I add them up according to the formula, the virtual sites seems out of the plane of the other three particles. Where did I go wrong?
Thank you very much in advance,
Have a nice day
I can’t see why you think the virtual sites would be out of plane. The site it constructed as an offset from r_i where the offset is a linear combination of two difference vector with r_i. So it must be in the ijk-plane.
If the origin is not in the same plane as ijk, then the front part of this equation will be in the ijk plane, but adding the vector r_i to the equation cannot guarantee that the resulting vector will still be in the ijk plane.
The origin is r_i, so by definition in the same plane as ijk.
I get it, thanks a lot!
