[gmx-users] MSD

[afsaneh maleki]

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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