[gmx-users] VDW radii of Br and K+

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 25 08:59:39 CEST 2010

On 2010-08-24 22.53, nishap.patel at utoronto.ca wrote:
> Hello,
> I converted a .tpr file for Bromine ion and Potassium ion using -mead
> option and editconf. It gives out the Van der Waals radius of the atom,
> but I don't understand why i got ~2.46A for Potassium and ~2.31A for
> Bromide. Isn't the bromide ion bigger than Potassium? And I used genion
> to add both the atoms.
This is a force field quirk. From the oplsaa.ff/ffnonbonded.itp

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
opls_402  Br- 35 79.90400    -1.000       A    4.62376e-01  3.76560e-01
opls_408  K+  19 39.09830     1.000       A    4.93463e-01  1.37235e-03

You see that K+ has larger sigma than Br-.

> Thanks.
> -Nisha P

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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