[daisuke]

Dear developers and support team,

I am always enjoying using your software. I am conducting a MD simulation for a 20-mer antimicrobial peptide in the presence of a lipid membrane bilayer, following the guidelines in Tutorials 6.1 and 6.2. Currently, I am attempting to analyze the distance between the centroid of the peptide and the plane sandwiched by the lipid bilayers. Should I employ the trj_analysis tool for this analysis? If so, how should I define the groups in the [SELECTION] section? Alternatively, is there another method I could use?

Thank you in advance for your assistance.

Best regards,

[ckobayashi]

Hello,

Do you mean the distance to the “plane” between the upper leaflet and the lower leaflet?

If so, there is no tool in GENESIS that calculates such distance.

If the region between the upper and lower leaflets is not a clear plane,  I don’t think the definition of the distance is clear.

 

Sincerely yours,

 

Kobayashi