[ghemical-users] MD trajectories

Joshua Baraban joshua.baraban at yale.edu
Sat Mar 3 16:32:55 EST 2007


	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?

	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?

Thanks for your help,


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