[gmx-users] problems creating mixed solvent systems
Origamisven at web.de
Fri Aug 29 08:53:33 CEST 2008
> What might be worth trying is starting with genconf. Use genconf -nbox (and
> -dist, if necessary), starting from one MeOH molecule to generate a grid of 400.
> Then use genbox with -maxsol (and perhaps playing a bit with box dimensions).
Thanks for your perspective, I really appreciate it
I was trying around with that when I finally thought of a viable solution on my own, which actually seems to work (still simulating)...
I'll put it here because I didn't find anything on the archives about creating mixed solvent systems and it may be of use to somebody:
--> start with small box of given ratio (10 molecules 2moh:8water using single molecule moh.gro and spc216.gro from gmx top directory)
genbox -ci moh.gro -nmol 2 -box 1 -o test.pdb -seed 5
genbox -cp test.pdb -cs spc216.gro -maxsol 8 -o test2.pdb
--> set density lower than expected value to avoid clashes
editconf -f test2.pdb -o test3.pdb -density 800
--> solvate system using small box as solvent
genbox -cs test3.pdb -box 3.9 -o test4.pdb
--> adjust box size so more than the necessary molecules are in the box
--> MANUALLY delete surplus molecules in the coordinate file
editconf -f test4.pdb -o 200moh_800wat.gro -density 950
--> set proper density to experimental values
I haven't analyzed the result but at least the clashes are finally gone.
I suppose boxes like this need to be equalibrated for a long time to insure a random distribution of molecules.
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