On 6/15/12 4:08 AM, Satish Kamath wrote:
Dear Users,
I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene
at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen
bond distance using g_hbond and it comes to 0.267 nm. I've also calculated
the density and it comes to 1229 kg/m3 (solid density = 1120 kg/m3 at 300 K
!!! Comments please...).
It seems that your model is rather poor. If your liquid is more dense than your
solid (and you're not water!) then it's not a very good representation.
I wanted to know if there are other properties that can be calculated to
validate my simulations. Justin in his paper J. Chem. Inf. Model. 2010, 50,
2221–2235, talked about calculating the enthalpy of vaporization using the
formula
∆Hvap = 〈Egas〉 - 〈Eliquid〉 + RT
I wanted to know how to apply this in simulation? Assuming I know the
boiling, do i simulate at that temperature until liquid becomes vapor? How
will I know that the liquid has vaporized.
The calculation above does not imply that you cause the liquid to boil. You
need two simulations - liquid (condensed) and gas. The details of what we did
are in the paper and in the Gromos96 references that have been published over
the years. This topic has also been discussed at length in the mailing list
archive, so I would encourage you to look for the threads.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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