[gmx-users] problems creating mixed solvent systems

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 28 11:56:58 CEST 2008

Ted Fischer wrote:
> 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

Your approach doesn't leave much room for the insertion of molecules, would be 
my guess.

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).


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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