Comparing mdp files and how to create a silica surface

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question:

Hi,

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.

Many Thanks,

Amo

2

Nonbonded settings differ because different force fields require different cutoffs, treatment of short-range forces, etc. If you built something with CHARMM-GUI, the .mdp files it provides will look quite different from the tutorial files because CHARMM and GROMOS force fields are very different in their treatment of nonbonded interactions.

It can do that too. Use the Nanomaterial Builder: CHARMM-GUI