Re: Question about Van der Waals radii

From: Peter Freddolino (
Date: Mon Jun 26 2006 - 10:57:21 CDT

To be a bit more clear (sorry), the time to get worried is if you start
seeing vdw interactions that are around the covalent bond distance
(usually 1-2 angstroms) -- this is a much better representative of what
you would intuitively think of as the sum of atomic radii. The VDW radii
are parameterized to give realistic energies for nonbonding interactions
at various distances, but they don't represent a clear physical quantity.

Peter Freddolino wrote:
> 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.
> Peter
> 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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