[gmx-users] VDWradii.dat

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 30 20:43:49 CEST 2010

nishap.patel at utoronto.ca wrote:
> Hello,
>    I have a question about how gromacs assigns VDW radii for ions. I 
> checked the vdwradii.dat file but it does not mention any ions, so where 
> do the parameters for ions come from? I got the .pqr file for sodium and 
> I got the atomic radii of 1.6652A, I am not sure where that value came 
> from.

Neither can anyone else unless you provide the command you gave that produced 
this result as well as the force field you're using.  Presumably you generated 
your .pqr file with editconf?  In that case, have a look at the code starting 
around line 587 (in the 4.0.7 source) for the decision structure that dictates 
how the value of "vdw" is assigned.


> I would really appreciate some help!
> Thanks.
> -Nisha P


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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