GROMACS modification: Yes/No
Here post your question:
I am new to Gromacs and due to the coronavirus have had to alternate my research project to a computational based study and have completed some of the tutorials to gain practice and understand the program. I have generated an mdp file for a protein molecule and membrane using CHARMM GUI and Gromacs. I would like to compare the mdp. file for the final production run against the mdp file for the protein membrane (KALP - 15 in DPPC) tutorial in Gromacs. What are the main things I should looked out for in an mdp file that provide really important information about the system and enable me to elucidate the difference between the two?
Secondly, for my project I will be using insulin (as monomer, dimer, hexamer) on one OH terminated surface versus one hydrophobic surface; simulating the influence of pH by varying the charge on insulin/the OH terminated surface.
How would I approach the creation of a terminated surface?
I have accessed CHARMM GUI and this allows for the creation of membranes, monolayers…etc but I would like to create a silica surface?
I have found relevant papers that have provided their model databases and can use these too but can I manually create my own?
I would really appreciate any help or advice to further my understanding.