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? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
