> In the absence of PBC, you simply have an infinite system. In a loose > sense, that may be NVT, but V is infinite, so whether or not you can > consider that to be constant or not is theoretical math above what I know :)
A real molecule in vacuum is usually NVE -- it is not coupled to the environment, and thus must have conserved energy. You can certainly add a thermostat, and then it will be NVT, though it won't be very much like a real isolated gas molecule. If you try to run NPT, the simulation will likely crash because of numerical instabilities, and there's not much of a point, since you are essentially either 1) in the ideal gas limit if running with no periodic boundary conditions 2) in some sort of weird superdilute crystal that really doesn't resemble anything real if run with a periodic boundary conditions If you are subtracting out the center of mass motion, then V is not infinite -- you remove the center of mass degree of freedom, and thus you have a very different ensemble than if you include the center of mass motion. You would need to multiply by V to get the partition function for an actual gas. Note that I would strongly suggest sd as the integrator/thermostat, since there are real issues with ergodicity in systems with only a few degrees of freedom -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
