GROMACS version: 2022
GROMACS modification: No
How is the van der Waals radius defined in GROMACS? I found file vdwradii.dat, where I have information.
; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; ‘???’ or ‘*’ matches any residue name
; ‘AAA’ matches any protein residue name
; Source: van der Waals radius - Wikipedia
; These come from A. Bondi, “van der Waals Volumes and Radii”,
; J. Phys. Chem. 68 (1964) 441-451
??? H 0.12
??? C 0.17
??? N 0.155
??? O 0.152
??? F 0.147
??? P 0.18
??? S 0.18
??? Cl 0.175
I know for every atom type we have sigma parameter, but can we say vdW radius=sigma?
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_001 C 6 12.01100 0.500 A 3.75000e-01 4.39320e-01 ; SIG
The van der Waals radius is itself an approximation of a sort, since atoms are not hard spheres in reality. Different experimental methods of estimation yield different values for the same species. One could say the LJ sigma parameter is in the same order of magnitude as the vdW radius, but sigma should be picked to produce the desired interatomic distance or some other property in the simulation, rather than precisely equal to the vdW radius. So probably it is not just
Besides, when visualizing, each program probably has its own vdW radius defined, right? E.g. Pymol has a specific. I just want to calculate the total vdW area for a molecule and I want to know what values to take