[gmx-users] VDWradii.dat

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon Aug 30 21:03:56 CEST 2010

Also, I am using OPLS-AA force field with TIP3P water

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On 2010-08-30 20.32, 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.
>> I would really appreciate some help!
>> Thanks.
>> -Nisha P
> Did you get the pqr file from editconf? Then read editconf -h.
> Check the -sig56 option.
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
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