GridMAT-MD: Input options for small amphiphilic molecules

User discussions
1

Hello,

I am using GridMAT-MD to calculate the area per lipid (APL) in a bilayer system that contains an additional amphiphilic molecule (around 1064 Da) inserted between the leaflets. Since this molecule is not a standard phospholipid, I set the input option protein = yes so that GridMAT-MD would treat it as a non-lipid species.

However, when I do this, I observe a large decrease in the calculated APL of the surrounding lipids. I am trying to understand if this effect is a genuine physical consequence of the inserted molecule or if it is an artifact of how the program excludes non-lipid species from the calculation.

My questions are:

  1. Is it correct to use the protein = yes setting for an inserted non-lipid amphiphilic molecule?

  2. Is it reasonable to observe a significant decrease in APL under these conditions, or does this suggest a limitation of the method?

Any clarification on the best practice for handling non-lipid amphiphiles in GridMAT-MD would be greatly appreciated.

2

This isn’t a GROMACS question; please email me to discuss. The program should detect anything as “protein” that isn’t either the defined lipid residue name(s), solvent, or ions. It will print the number of atoms it finds within the top and bottom leaflets of the membrane to the terminal, which is how you can check if it’s working.