Re: [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
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[gmx-users] Regarding TMAO model in gromacs

[Dilip H N]

Hello,
1] I want to know which is the model of TMAO molecule that is present in
charmm36 FF ..??
2] How can i use the Kast, Netz, Garcia, etc models in gromacs .. (when i
referred the literature i came across the different models of TMAO and the
charges, sigma, epsilon values are different from the above-mentioned
models with respect to .rtp, ffnonbonded.itp files in charmm36 FF. )
Do i need to make changes in the .rtp files to incorporate the other models
?? or any other way..??
So how can i solve this issue...

Any suggestions are appreciated

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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