[gmx-users] Simulating Multiple Solute Particles

Mark Abraham mark.j.abraham at gmail.com
Sat Oct 25 12:10:25 CEST 2014

On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz <nhoutz at purdue.edu> wrote:

> Hello, I apologize for any ignorance but I'm quite new to gromacs and am
> confused about a few things.
> I want to run some simulations of a small molecule, tetrolic acid
> (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a
> united atom approximation on the methyl group is sufficiently good for
> saving a bit of computation time. I have created a .gro file and a .top
> file and attempted to put it into gromacs but I don't know how to model
> more than one molecule of TTA. All of the tutorials I've looked up involve
> solvating enormous proteins and they only do one at a time. I'd like to
> simulate hundreds of TTA molecules with an appropriate amount of water
> molecules. I attempted to do this by specifying the numbers of TTA and H2O
> in my topology file, but when I tried to solvate it, gromacs removed the
> line specifying how many waters and replaced it with its own number (216)
> and made the box way too small to fit any more TTA. I feel like this may be
> trivial, but I'm stuck. I really appreciate anyone's help.

You can adapt http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
to do this.

> After I figure this out, I'm going to try do dissolve tetrolic acid in
> chloroform, then ethanol as well. I suspect gromacs doesn't have a built in
> .gro or .top files for either of those (certainly not chloroform). Would
> the solvate command work just as well if I created my own?

Yes, but perhaps gmx solvate -p won't quite do what you want. Do equilbrate
that box decently; garbage in -> garbage out.


> Thanks in advance!
> N.H.
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