[gmx-users] fluxer.py MARTINI

[shivangi nangia]

Hello All,

I have a question about MARTINI's fluxer.py.

I do realize that this might not be the exact place to ask this but it will
be really helpful is someone can answer these questions


link to complete description of fluxer.py :
http://cgmartini.nl/images/parameters/local/fluxer/fluxer.py)

1) Is there any paper on this (like there is one on insane.py)

2) The description says "this tool calculates fluxes across either a whole
bilayer or through a defined channel. The trajectory must have been treated
with -pbc nojump and, if analyzing the flux through a channel, care must be
taken to ensure the channel is kept whole in the trajectory (use -pbc
cluster)."

For throughout the membrane the trajectory should have been treated with
-pbc no jump and for channel  the trajectory which as been treated with pbc
-nojump is treated further for clustering OR one just takes the
raw/untreated trajectory and then just do clustering.

3) I have been trying to look at water flux through a pore formed by
transmembrane bundle/oligomers of peptides. I had just treated the raw
trajectory once by just clustering the peptides together (-pbc cluster; did
not do pbc -nojump). Also, I defined the delimiting groups as: first
residue of the transmembrane protein as "top" and the last residue of the
transmembrane protein as "bottom" and have tried to used various "-mult"
options but everytime I get zero flux (which I can see is there visually in
VMD).
The description to use this says "When analyzing a single channel, the
option -mult can be passed to restrict counting to the cylinder of radius
mult*RoG, where RoG is the radius of gyration (not mass weighted) of the
delimiting groups. Care must be taken to ensure these groups remain whole
for the whole trajectory."


Kindly assist.

Many thanks in advance,
sxn