Hello awesome people,
I am new to GROMACS and i have been practicing with different tutorials available online. I successfully ran 1ns simulations. I ran couple of simulations with mdp files as they were, just to test everything how things works i also did modify some of the parameters. There are too many parameters defined and i don't understand everything in the mdp files (i am still exploring). it would be very helpful if someone just summarizes the important parameter's i should be looking at while carrying out next my simulation.
Thank you very much in advance
Hi. Read the gromacs manual. You can know the details about each parameters in the mdp file. You can go through below link. I think it'll be helpful.
http://manual.gromacs.org/current/online/mdp_opt.html
Trying to summarise the scope of the run parameters of Gromacs is very difficult, there are so many! Even when you look at a reduced number e.g., in the case of an energy minimisation, the actually grompp process will include many more default values that you aren't aware of until you look through your simulation log file. Changing anyone of these parameters is also very dependent on what you are trying to do. For example, free energy calculations, different ensemble calculations, electrochemistry (I think!), simulated annealing - the list goes on.
As you are new to Gromacs I would highly recommend going through these tutorials:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
That is where I started with Gromacs seven/eight years ago. Go through each tutorial in turn, and refer back to the Gromacs manual. This is a learning curve that only you can climb.
You should keep in mind that many parameters are implied by the force field. I'd suggest using the same set as in the force field original paper.
Others (such as temperature, pressure, electric fields) you can modify accordingly with the purpose of your simulation.
I found in this page a guide for each parameter
http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
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