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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--
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
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