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

[David van der Spoel]

Arneh Babakhani wrote:
> 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?
you could do it if you wish, although you should check literature first. 
alternatively you could rely on combination rules.

> 
> 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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>>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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