Hi, I am working on the simulation of protein memberane.
How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need “index file” that is included phosphate atoms within 0.35 nm of protein. how can I obtain this index file thanks in advance, Afsaneh Maleki
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