Dear all, The only tutorial on umbrella sampling by Justin ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html) assumes a rectangular box and pulling is done to separate chains. Is it true that the approach worked solely because one of the reference chains was position restrained as that did not allow it to rotate. regards, cyrus
On Sun, Jul 7, 2013 at 4:45 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 > -- 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
