[gmx-users] Simulating Multiple Solute Particles

Dr. Vitaly Chaban vvchaban at gmail.com
Sun Oct 26 07:46:51 CET 2014

Hi -

genbox must work. You add the first molecule, then the second molecule
and so on. So, I suggest to run genbox for a few times and have enough
empty space available in the box. Otherwise, there is a wonderful tool
called PACKMOL.

The acid molecule looks pretty sexy. I guess it will not be very
straighforward to capture the effect of the triple bond right near
carboxyl group.

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН

On Sat, Oct 25, 2014 at 8:23 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.
> 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?
> Thanks in advance!
> N.H.
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