solvation in moltemplate

Dear Ali

   Alas, moltemplate can not automatically solvate a molecule. (Other
basic features which are missing: It also can not automatically create
bonds between nearby atoms, or handle huge systems: >> 10^6 atoms).

   However if the molecule has a reasonably simple shape, you can
usually use the "delete" command to remove water molecules near your
solute molecule.

   For example: I have attached a file where I built and solvated the
great pyramids of Giza! The distance units used in the water
molecules and the bricks in the pyramid are somewhat incompatible. No

   I use the "delete" command to remove water molecules which are too
close to "Bricks" in the pyramid. The relevant lines (from
"") are reproduced below:

delete wat[3-17][3-17][4] #delete a 15x15 2-D square
delete wat[3-17][3-17][5] #delete a 15x15 2-D square
delete wat[4-16][4-16][6] #delete a 13x13 2-D square
delete wat[4-16][4-16][7] #delete a 13x13 2-D square
delete wat[5-15][5-15][8] #delete a 11x11 2-D square
delete wat[6-14][6-14][9] #delete a 9x9 2-D square
delete wat[7-13][7-13][10] #delete a 7x7 2-D square
delete wat[7-13][7-13][11] #delete a 7x7 2-D square
delete wat[8-12][8-12][12] #delete a 5x5 2-D square
delete wat[9-11][9-11][13] #delete a 3x3 2-D square
delete wat[10][10][14] #delete a single water molecule
delete wat[10][10][15] #delete a single water molecule

As always, you will have to minimize and equilibrate the system first.
(If empty cavities/bubbles appear that probably means you have
deleted so many water molecules that the water can not find the
solute. Try to avoid that. In this example, I get bubbles because I
deliberately turned off Van-der-walls interactions between the two
"molecule" types.)

README_visualize.txt (3.08 KB)




VMDsolvate_p+w.jpg (2.78 KB) (15.8 KB) (1.43 KB)