Re: Question about Van der Waals radii

From: Peter Freddolino (
Date: Mon Jun 26 2006 - 10:49:09 CDT

Hi Chandra,
you might want to have a look at the VDW potential again; while the
energetic minimum does indeed occur at the sum of radii, there is still
a region inside of this radius that has fairly easily accessible energies.

Chandra Ramananjara wrote:
> Hi all,
> I have done a simulation of ion in water and I notice something
> strange when I examine the dcd trajectory files. For example, in some
> frames, I notice that the center-to-center distance between the ion
> and a particular oxygen is less than the sum of the van der waals
> radii of the ion (sodium) and oxygen (OH1). It doesn't make sense
> intuitively that the sodium ion and the oxygen atom should be
> overlapping.
> I found the values for van der waals radii of sodium ion and oxygen in
> the "nonbonding interactions" section of the widely available CHARMM
> parameter file 'par_all27_prot_lipid.inp'. This file lists the van der
> waals radius of OH1 (oxygen) as 1.77 and the van der waals radius of
> sodium ion (1.36375) and yet some frames in my trajectory file contain
> cases where the sodium-oxygen distance (measured from their centers)
> is less than 1.77 + 1.36375
> Is this normal ?
> Thanks,
> Chandra
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