GROMACS version: 5.4
GROMACS modification: Yes/No
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Dear all,
I hope this email finds you well. I am a new user of gromacs and need it to evaluate the interaction between a molecule and water (4-site water model).
I have the topology file of water (without any solute) as well as itp file of the solute.
How can I have the topology file of the interacting system of “solute in the water”?
I just know I should include the itp file and add the solute in the [molecules] but I do know how I should consider the LJ interaction of solute and water.
As I am a beginner, I really got confused with a lot of complex commands as well as available documents of gromacs and really appreciate your help :D
My first suggestion would be that if you are starting to use gromacs to use the most recent version, 2022.1, and not the ancient version 5.4. Secondly, the tool you want is gmx insert-molecules. Please read the documentation on this to figure out what to do next.
Welcome to gromacs community. Feel free to ask any question you have. Also try to google your question with added text ‘gromacs forum’ at the end, to find answers to similar questions asked before.
Coming back to your question: the LJ interaction is embedded in atom type defined for every atom in the itp. So when you are combining both itps in topology file, at the back end LJ cross interaction between the every atom of topology file is taken care of. So you need not to worry.