Dear All, I created a simulation box in editconf with -d 2.5. Then in genbox, I used the -shell 1.4 option to define a 1.4 nm thick layer of solvent around my protein. When I visualized the system in Rasmol, as expected, there was a lot of "empty space" in the simulation box. Should this vacuum create any artifacts in PBC or other energy calculations? I did not receive any warnings or messages and so continued with the MD simulation.
During the MD, I saw that some ( <10) water molecules travel away from the shell/layer around the protein and come to lie in the vacuum of the box. Correspondingly the box size also varies depending upon the presence of such water molecules. After about 60 ps, the box reduced in size to just accommodate the solvent shell around the protein. And as yet the solvent forms a layer around the protein and is not distributed evenly in the box. By 100 ps the solvent molecules no more form a layer but are distributed evenly within the box (cube) One last observation is that when I viewed this trajectory in VMD, the molecule seemed to translate in space. There's no option to view the unitcell in VMD, so I do not know whether the whole box is shifting or just the protein+solvent is shifting inside the box. Please let me know whether these observations are acceptably normal. Thank you Aditi Borkar, Tata Institute of Fundamental Research, Mumbai. _______________________________________________ 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/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/mailing_lists/users.php
