[gmx-users] Non bonded parameters for Xe Xe Interactions

Arneh Babakhani ababakha at mccammon.ucsd.edu
Fri Jun 29 00:32:26 CEST 2007

Great thanks, I had no idea such a tool existed. 

Also, if we're doing Xenon in water (spc) simulations, we have to 
parameterize the nonbonded interactions between OW and Xe, and H and Xe, 
right?  That parameterization doesn't already exist, or does it?

David van der Spoel wrote:
> Arneh Babakhani wrote:
>> Hi GMX community,
>> We're doing some MD involving Xenon atoms.  For our parameterization, 
>> we obtained sigma and epsilon (over kB) values of 3.975 Ang. and 
>> 214.7 K, from the following JCP reference:
>> http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000120000014006674000001&idtype=cvips&gifs=yes 
>> We then calculated the C6 and C12 nonbonded parameters for a Xe Xe 
>> interaction, based on combination rule #1, as specified on page 88 of 
>> the GMX manual.  We obtained: C6 = 0.0282  and C12 = 1.11e-4
>> Does this look reasonable?  Are there others out there that have done 
>> Xenon MD, willing to share their nonparm. numbers?
>> Thanks,
> go to your gromacs source code, src/contrib and type make sigeps. This 
> little program will do the conversion for you. Otherwise, check the 
> manual, chapter 4.
>> Arneh
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