[gmx-users] Meaning of the screen output "largest charge group radii "

Agnivo Gosai agnivogromacs14 at gmail.com
Wed Mar 2 21:21:27 CET 2016

Hello Users,

I am using AMBER99SB-parmbsc0 ff and in my mdp file I put the cut-off as
1.4 nm

However, during grompp and mdrun command execution this message is written
in the screen output file :

Largest charge group radii for Van der Waals: 0.040, 0.040 nm
Largest charge group radii for Coulomb:       0.079, 0.079 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 64x64x128, spacing 0.116 0.116 0.116

What is with the this charge group radius ? Is this system specific or does
this depend on the ff only? I read the original AMBER99SB paper and found
that they used a cut-off of 0.8 nm for all non-bonded interactions.

Please explain.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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