On Sun, Jul 7, 2013 at 4:15 PM, akcyrus <akcy...@gmail.com> wrote: > Dear all and Tsjerk Wassenar, > I could not grasp how a rectangular box will be a problem. Lets assume a I > have a cylinder of radius r (nm) and height h (nm) with h>r. I place the > cylinder aligned along z-axis and then in a rectangular box with dimension > 2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem > could be when during simulation, the cylinder gets aligned parallel to XY > plane and the box vectors are shorter along X and Y,isn't that right?
Yes. If that can happen, then your simulation will become junk when it does. > Also > during the simulation, with isotropic pressure coupling the box tend to be > cubic and this would also cause problems. Correct me if I am wrong or don't > understand it right. Anisotropic coupling is available. But I don't think that is an issue in choosing whether a rectangular box is plausible. Mark -- 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
