[gmx-users] Regarding TMAO model in gromacs

[Miner, Jacob Carlson]

One way to incorporate these models is to create a folder that has all of the relevant parameters you need (.rtp, .itp, etc.).
I simulate specific force fields (including the Osmotic TMAO model) by this folder within the directory where I am simulating and then I generate .gro files and .top files that call from these data sets.

So my .top file calls my .itp file within the relevant directory (name-of-my-folder.ff/):

Within .top:
"
#include name-of-my-folder.ff/TMAO.itp"
"

This file in turn contains bonded interactions [atoms], [bonds], [angles], [dihedrals]

For the non-bonded interactions (nonbonded.itp, within name-of-my-folder.ff/), I include its name in the forcefield.itp file therein and call the forcefield.itp file from the .top file.

Within .top:
"
#include name-of-my-folder.ff/forcefield.itp"
"

Within name-of-my-folder.ff/forcefield.itp:
"
#include "nonbonded.itp"
"

This serves to organize all of the different potentials in one folder that you can then call with your .top files.

Jacob Carlson Miner
Postdoctoral Research Associate
Theoretical Biology and Biophysics (T-6)
Los Alamos National Laboratory