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? 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. regards, akcyrus
On Sun, Jul 7, 2013 at 12:00 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Cyrus, > > In a rectangular box (which is a specific case of a triclinic box) your > molecule can't rotate freely without significant chance to run into its > periodic image, invalidating whatever result you get. So, unless rotation > is of no concern, or can be cirrcumvented, you'll need to use a rhombic > dodecahedron. > > Cheers, > > Tsjerk > > > On Sun, Jul 7, 2013 at 11:25 AM, akcyrus <akcy...@gmail.com> wrote: > > > Dear all, > > I am planing to do pulling on a bundle of elongated proteins. I compared > > two box types - triclinic and > > dodecahedron. The volume and total number of atoms (protein+solvent), > > following the editconf and genbox commands, > > were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 242222 > for > > dodecahedron. > > Although dodecahedron box has always been suggested due to shortcomings > in > > the periodic interactions for a triclinic box, but > > I have seen examples of the use of triclinic box. Due to this huge > > difference in the number of solvents in the two cases > > I am tempted to use triclinic box, but I am a bit confused. Any ideas or > > suggestions? > > regards, > > cyrus > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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