How to find diameter of an atom in gromacs?

User discussions
1

Dear all,

How can I find the radius of one (Br-) ion in my polymer/water/ion system in Gromacs? I used the OPLS-AA force field.

Thanks

2

Hi,

Atoms don’t have well determined radii to calculate unless you are running hard sphere simulations, but OPLS-aa (and I believe all force fields implemented in Gromacs) uses soft potentials.

You can estimate the “space” taken up by your ion on average using e.g. the radial distribution function to other atoms (gmx rdf). Or you might be able to estimate its Van der Waals radius (not to be confused with an actual atomic radius, which does not exist) using other methods, check the literature.

Regards,
Petter

3

Dear @pjohansson

Thanks a lot for your help. I think the sigma of Lennard-johns potential gives the van der Waals radii with appropriate accuracy. However, I was looking for a direct way using Gromacs commands.

Thanks again

Regards,
Mohammad