Hi, I want to simulate a water soluble protein of approx. 160aa size and its shape from a .pdb looks a little elongated (if rotated around the longest axis, it roughly occupies a cylinder with length to diameter ratio 1.8 - 1.9). Would it be considered globular enough to try dodecahedron box?
Out of curiosity, I compared the triclinic and dodecahedral boxes created for my protein. After I created a triclinic box with g_editconf, I got this: Read 2406 atoms Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons No velocities found system size : 4.830 3.541 4.901 (nm) center : 19.439-14.327 13.948 (nm) box vectors : 4.830 3.541 4.901 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 83.82 (nm^3) shift :-16.024 17.097-10.498 (nm) new center : 3.415 2.771 3.451 (nm) new box vectors : 6.830 5.541 6.901 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 261.17 (nm^3) Dodecahedron: Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons No velocities found system size : 4.830 3.541 4.901 (nm) diameter : 5.907 (nm) center : 19.439-14.327 13.948 (nm) box vectors : 4.830 3.541 4.901 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 83.82 (nm^3) shift :-13.508 20.257-11.153 (nm) new center : 5.931 5.931 2.796 (nm) new box vectors : 7.907 7.907 7.907 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume : 349.61 (nm^3) So from the box volumes I see that in this case a triclinic box is a preferred choice. However, as I am aware that dodecahedral box representation (as seen in VMD for example) is subject to periodicity effects, I am not completely sure if exactly these box sizes will be used in simulations. If not, how could I estimate the actual box volumes before I start simulation (to maximize performance)? And I have one more short question: Is it possible somehow to visualize the "actual" dodecahedral box at this stage (i.e. right after adding water, having no trajectory file yet)? Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/Actual-box-size-tp5003850.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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