Dear Mark, Thank you. I was indeed using pressure coupling.
My protein is crescent shaped so if I use a regular simulation box, I get one with a large volume. I hoped that using a shell will reduce the number of atoms in the system and will facilitate computation. So should I just stick to the traditional way of using solvent boxes to proceed with the simulations? Is there an alternative? Thank you. On Tue, Sep 22, 2009 at 6:45 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Aditi Borkar wrote: >> >> 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. > > Why did you define a spherical shell inside a periodic box? This will get > the worst of all worlds - periodicity artefacts, finite-size effects and > boundary effects. > >> 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. > > That's normal. > >> 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) > > The box will only change size if you are using pressure-coupling, but you've > not told us about this. > >> 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. > > The whole box can't shift... it's periodic, and there's no preferred unit > cell. If you'd prefer a particular arrangement of box and atoms then you > need to read trjconv -h, consider the various options and experiment until > you're happy. > >> Please let me know whether these observations are acceptably normal. > > It seems very unlikely that you have both the simulation you hoped you'd > have and a successful simulation :-) > > Mark > _______________________________________________ > gmx-users mailing list gmx-us...@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 > -- 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