[gmx-users] problems creating mixed solvent systems

Ted Fischer Origamisven at web.de
Thu Aug 28 11:14:08 CEST 2008

Good day to you! 

I'm new to MD and this is my first time bugging you with issues I don't seem to be able to solve on my own (using the archive and the manual), so I hope you bare with me and can possibly offer me a sanity check or some alternative approaches to my problem.

As I have already indicated, I want to set up boxes of mixed solvents with a fixed ratio (and density) and have tried numerous approaches but always ran into difficulties, mostly due to clashes with the result of my system blowing up.

For example: I want to create a box with 400 methanol and 600 water molecules. 

The obvious choice to go about it is "genbox", using -ci/-cs/-cp and -maxsol/-nmol flags.

Most approaches looked something like this:

genbox -ci spc.gro -nmol 600 -box 3.9 -o temp.gro -seed 5
genbox -cp temp.gro -ci moh.gro -nmol 400 -o temp2.gro -seed 13
editconf -f temp2.gro -o temp3.gro -density 948.56

I seem to have tried every variation using genbox in order to achieve a viable system, also using the pre-equalibrated spc216.gro and methanol216.gro, but there were always too many clashes for minimization/equilibration to even start.

I then tried another approach, taking the same system of 1000 molecules, starting with a box of 1000 methanol molecules (using methanol216.gro) and manually (well by macros) changing 600 methanol molecules to water molecules with the same coordinates.

It occured to me that the bond lenght of these water molecules are now a problem, but I was hoping that the charge difference would fix just that (I thought -DFLEXIBLE would help). - Am I making sense here?

My aim is to have a fairly simple and time-efficient way of doing things, because I will need to be flexible with the choice of solvents.

Any feedback would be highly appreciated. Thanks in advance...
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