[gmx-users] How the pressure is computed

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 14 01:52:05 CET 2012

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


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