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FLuxer.py
- sxn
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8 years 1 month ago #5420
by sxn
FLuxer.py was created by sxn
Hello,
I have few questions about 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 is that the trajectory which as been treated with pbc -nojump is treated further for clustering OR one just takes the raw/untreated trajectory and then do clustering.
3) I have been trying to look at water flux through a pore formed by transmembrane bundle of peptides. I had just treated the raw trajectory once by just clustering the peptides together (-pbc cluster). 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
I have few questions about 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 is that the trajectory which as been treated with pbc -nojump is treated further for clustering OR one just takes the raw/untreated trajectory and then do clustering.
3) I have been trying to look at water flux through a pore formed by transmembrane bundle of peptides. I had just treated the raw trajectory once by just clustering the peptides together (-pbc cluster). 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
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- mnmelo
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8 years 3 weeks ago #5481
by mnmelo
Replied by mnmelo on topic FLuxer.py
Hi, and sorry for the delay in replying.
Your procedure seems correct, but pay attention that the 'top' and 'bottom' groups must represent a sort of a ring, or portal, to define the entrance of your channel. If you select a single residue for 'top', it won't work.
If all your transmembranar peptides align in the same fashion (say, N-terminus up, C-terminus down), then selecting all first residues for 'top', and all last for 'bottom' will work.
The -mult option just applies a factor to the channel cylinder fluxer.py interprets from your 'top' and 'bottom'. If -mult is 1, then a cylinder with the same radius as the average RoG of 'top' and 'bottom' will be used. For -mult 2 you'll get a cylinder twice as broad.
For 'top' and 'bottom' I typically pick residues just before and after the channel's constriction and, if the channel has a marked hourglass shape, set -mult to around 1.5. But there should be no problem with choosing 'top' and 'bottom' closest to the channel's edges, like you do.
Finally, this script must be able to tell that a molecule crossed through the channel. It is therefore useful to have relatively frequent trajectory frames (say, 0.5ns apart, but this very much depends on your system) so that at least one frame with the molecule within the channel is available. If your frames are spaced too much you might miss out on these events since there's no way to know whether the molecule crossed the membrane via the channel or just across the membrane.
Let me know if this helps,
Manel
Not yet. We'll update relevant information when it is out.1) Is there any paper on this (like there is one on insane.py)
I'm not sure I understand what you're asking, so I'll just describe what you should do:For throughout the membrane the trajectory should have been treated with -pbc no jump and for channel is that the trajectory which as been treated with pbc -nojump is treated further for clustering OR one just takes the raw/untreated trajectory and then do clustering.
- - Center the membrane in the z-center of the box; if you have a channel to analyze, center on it instead;
- - Remove the pbc;
- - Remove jumps across the pbc; The membrane should remain in the same z position, since, after step 1, it shouldn't ever cross the z-boundary.
3) I have been trying to look at water flux through a pore formed by transmembrane bundle of peptides...
Your procedure seems correct, but pay attention that the 'top' and 'bottom' groups must represent a sort of a ring, or portal, to define the entrance of your channel. If you select a single residue for 'top', it won't work.
If all your transmembranar peptides align in the same fashion (say, N-terminus up, C-terminus down), then selecting all first residues for 'top', and all last for 'bottom' will work.
The -mult option just applies a factor to the channel cylinder fluxer.py interprets from your 'top' and 'bottom'. If -mult is 1, then a cylinder with the same radius as the average RoG of 'top' and 'bottom' will be used. For -mult 2 you'll get a cylinder twice as broad.
For 'top' and 'bottom' I typically pick residues just before and after the channel's constriction and, if the channel has a marked hourglass shape, set -mult to around 1.5. But there should be no problem with choosing 'top' and 'bottom' closest to the channel's edges, like you do.
Finally, this script must be able to tell that a molecule crossed through the channel. It is therefore useful to have relatively frequent trajectory frames (say, 0.5ns apart, but this very much depends on your system) so that at least one frame with the molecule within the channel is available. If your frames are spaced too much you might miss out on these events since there's no way to know whether the molecule crossed the membrane via the channel or just across the membrane.
Let me know if this helps,
Manel
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