From: Chandra Ramananjara (mozart20d_at_yahoo.com)
Date: Mon Jun 26 2006 - 09:14:10 CDT
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 ?
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