I want to get the discussion started on this. For now I'm mostly referring to the virtual interaction sites supported by Gromacs (ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf) although I think some of these are supported by OpenMM as well.
I think right now, it's best to add support for the simple 2 and 3 site types and worry about the rest later.
What I'm trying to workout in my head is how these sites are going to get defined, as the virtual sites technically aren't bonded to their neighboring atoms.
Gromacs:
6 virtual site types (type2, type3, type3fd, type3fad, type3out, type 4fdn)
Add sympy expressions for various virtual site types
mattwthompson
commented
4 years ago
I want to get the discussion started on this. For now I'm mostly referring to the virtual interaction sites supported by Gromacs (ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf) although I think some of these are supported by OpenMM as well.
I think right now, it's best to add support for the simple 2 and 3 site types and worry about the rest later.
What I'm trying to workout in my head is how these sites are going to get defined, as the virtual sites technically aren't bonded to their neighboring atoms.
Gromacs:
** MORE INFO TO COME