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

[David van der Spoel]

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
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++