On Sat, 3 Mar 2007, Joshua Baraban wrote: > Hi, > > A few questions about MD simulations in Ghemical: > > How are the E_solute/E_solvent/E_solusolv calculated in MD > trajectories? Is there any way to manually set how the molecules in the > simulation are grouped as solvent and solute? Also, are there other programs > that can read .traj files? Can Ghemical export trajectories in a more > compatible format? Hello Joshua, and sorry for the late answer. In the future please join the mailing list and your posts will get through quicker. There is no exporting of trajectory file, and I'm not aware of other programs that could read it. The E_solute/E_solvent/E_solusolv -feature is not really complete yet ; I have added it for demonstration/teaching tasks of my own. The feature is also changed in the latest development version where a more advanced way of requesting energy components have been added. But there is no user interface for it yet. :( The old E_solute/E_solvent/E_solusolv works so that it should put the energy of hand-drawn molecules into E_solute and the energy of automatically added solvent molecules into E_solvent ; E_solusolv is their interaction energy terms. > Do the solvate commands set up periodic boundary conditions (PBC)? > If not, what are the purple lines, and can PBC be added? Why aren't they > (the purple lines/PBC) saved in .gpr files? The solvate_box command sets up the periodic boundary conditions information. To make these settings effective you must setup the computations so that the computation "engine class" is compatible with the settings ; so you must select the "engine class" with name "the periodic engine (minimum image model)" or otherwise the settings are simply ignored. The settings are not yet saved in .gpr files but are (I hope) some day in future. The reason for the above is that I have not had time to make it any better; it could be done better and I wish to do it better but I have no time to do it better right now. Regards, Tommi