[gmx-users] specialized solvents

[Anton Feenstra]

From: "David Kendall" <dkendall at ameritech.net>
> 
> I am trying to create a solvent that has a lot of water and a little bit
> of impurity.  Something like 100 molecules of H2O and 1 CH4, but I am
> spinning my wheels trying to figure out how to do it.  Has anyone out
> there created their own solvents and could give me a HOW-TO on it?

IMHO it's fairly trivial: two ways to do it:

1) you generate first a box with the appropriate number of CH4 molecules
    (in united atoms, that's only one particle per molecule, so you could
    even do it in a simple text editor), and solvate that with 'pure' SPC
    water using genbox.
2) you generate an appropriate box of SPC water (or take spc216.gro, if
    that is already big enough for your purposes), and then change several
    water molecules to CH4. If you want explicit hydrogens, don't worry
    too much about their positions; they will EM to the right place in a
    few, or even single, step. If you're editing .gro, be sure to also
    change the 'natoms' line at the beginning.
It's smart to put your CH3 in one place, e.g. at the beginning, because
your molecules in the [molecules] section of your topology must be in
exactly the same order as in the .gro.

With your new 'solvent.gro' file, you can solvate your solute of interest
using genbox.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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