[gmx-users] Liquid/Gas Systems

[Justin A. Lemkul]

Fabian Casteblanco wrote:
> Hi Justin,
> 
> You had helped me earlier on calculating the heat of vaporization of
> methanol and it worked great.  I'm just trying hard to understand
> conceptually what is the difference between simulating a liquid phase
> and a gas phase in Gromacs.  I mean technically if we throw in 1000
> molecules of component A, would it only be a gas if we made the box
> super huge?  If we run NPT on a system, is that technically when we
> are compounding it together to find a liquid density?  I'm just a bit
> confused on the difference.  I've been simulating liquids up to this
> point so when I ran only NVT on a single gas molecule, I was trying to
> understand why we only run NVT on it (0 pressure so no pressure
> coupling).

The basic premise is that, in the gas phase, the gaseous species (atoms or 
molecules) do not interact (assuming an ideal gas), so yes, you absolutely could 
build a huge box that has N molecules in it to match your condensed phase 
system.  What tends to happen is that molecules will eventually find one another 
and form clusters, which really (I think) is just an artifact of using 
condensed-phase parameters to simulate a gas.  If the atoms/molecules find each 
other, they condense.  This type of simulation would have to be done under NVT 
conditions, since gases fill the volume of their container, right?  NPT would 
indeed just compress all of your particles together into a liquid.

The purpose of simulating just a single molecule in isolation is that it easily 
satisfies all the requirements of the ideal state.  The molecule is completely 
isolated and there are no periodicity artifacts.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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