[ghemical-users] MD trajectories

Tommi Hassinen thassine at messi.uku.fi
Tue Mar 6 02:44:40 EST 2007

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.



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