Hello again !
According to amber tutorial I found a possibility to compute the area per
lipids using :
vector test box out vector.dat
awk '{print $1, ($2 * $3) / N}' vector.dat > area.dat
My question: what is the easiest way to compute N (the total number of
lipids assuming that they are splitted on head-tail using amber ff) ??
Additionally I would like to calculates how the lipid density varies as a
function of distance from the protein using radial distribution:
radial 0.1 10.0 .CA,C,O,N,H :OL,PA,PC,PE,PS,CLI out out.xvg
which does not produce any output indicating error in the selected amber
masks
Many thanks in advance
Enrico
---------- Forwarded message ---------
Da: Enrico Martinez <jmsstarlight.gmail.com>
Date: mar 23 lug 2024 alle ore 10:58
Subject: Analysis of lipids in membrane generated by PackMol memgen
To: AMBER Mailing List <amber.ambermd.org>
Dear Amber users !
Dealing with the analysis of a membrane system composed of 5 different
lipids with embedded protein (the system was created using packmol) I would
like to estimate the equilibration of this membranes e.g. checking the
percentage of the mixing of the lipids, their lateral diffusion etc. Which
commands of cpptraj could be useful for such analysis ?
Many thanks in advance !
Enrico
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Received on Wed Jul 24 2024 - 07:30:02 PDT
