Andrew DeYoung wrote:
Hi,
I am running Gromacs 4.5.5. I am using an orthorhombic simulation box (all
box angles of 90 degrees: i.e., a rectangular prism) for which two of the
box vectors are approximately equal in length, but the third box vector is
much, much longer than the first two vectors:
Lz >> Lx ~ Ly
For example, my box vectors are Lz = 30 nm and Lx ~ 3 nm and Ly ~ 3 nm, so
my simulation box has approximate volume 270 nm^3. However, my system
occupies only a small fraction of the volume of my simulation box: my system
occupies only about (6 nm)*(3 nm)*(3 nm) = 54 nm^3. My system is terminated
at z=-3 nm and at z=+3 nm by large, periodic molecules (comprising a
membrane). Between these barriers of large, periodic molecules are many
small molecules (comprising a liquid).
The upshot of this is that a very large percentage of the volume is vacuum,
having no molecules. The reason for this is a trick, by which my system is
effectively two-dimensional; Lz is so long so that the system will not "see"
its own periodic image along the z direction.
But, my question is, what if I run an NPT simulation and then use g_energy
to print the system pressure as a function of time? Is the calculated
pressure: (1) the pressure calculated by taking into account the entire box
volume (270 nm^3), or is it (2) the pressure calculated by taking into
account only the volume of the box which is not vacuum, i.e., actually
occupied by molecules (54 nm^3)?
My guess is that it is pressure (1) that is being calculated, and printed to
the .edr file. Is this correct?
What if I would like to calculate the pressure (2), the pressure due to only
the non-vacuum part of the system? Is there a way to specify that only part
of the simulation box be taken into account when computing the pressure? Or
is there a way to calculate the "local pressure," just for that 54 nm^3 out
of 270 nm^3?
I suspect that within very few simulation steps, there will be no difference.
Under NPT, vacuum regions compress very rapidly.
You may need a different approach, for instance "pbc = xy" for an infinite
z-dimension. There are limitations to this approach, as stated in the manual,
but it may be more sound.
-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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