[gmx-users] Re: Positive Potential Energy after equilibration

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 15 12:37:41 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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