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
--
========================================
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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