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Using insane.py
- pela3247
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10 years 9 months ago #1798
by pela3247
Using insane.py was created by pela3247
Hi all,
I just discovered the very nice tool insane.py for constructing a martini cg-system from scratch, and have found it very easy to use.
I have however one question about how to make it generate a bilayer system with a given number of lipids in each leaflet.
From the help-text, it says that "if -d is omitted, those numbers are interpreted as absolute numbers", referencing the number of lipids in either leaflet I assume.
I have then tried both of the following, but I can't make the script produce a bilayer with the lipid composition and number of lipids that I want. I need a bilayer with 256 lipids in each leaflet, consisting of 75% POPC and 25% POPG. My command lines have been the following:
$ ./insane.py -o membrane_cg.gro -p membrane_cg.top -pbc cubic -box 13.78,14.27,11.11 -l POPC:192 -l POPG:64
This results in the output:
; X: 13.780 (18 lipids) Y: 14.270 (18 lipids)
; 324 lipids in upper leaflet, 324 lipids in lower leaflet
; Charge of membrane: -162.000000
; Total charge: -162.000000
So 324 lipids per leaflet in total, not 256. I assume it is no coincidence that 18*18=324 as well...
I prefer a cubic box, and my box-dimensions are from an atomistic system with the same constituents that I have already run.
I have also tried to take out all references to the box-size by running.
$ ./insane.py -o membrane_cg.gro -p membrane_cg.top -pbc cubic -l POPC:192 -l POPG:64
That gives the output:
; X: 2.500 (3 lipids) Y: 2.500 (3 lipids)
; 9 lipids in upper leaflet, 9 lipids in lower leaflet
; Charge of membrane: -4.000000
; Total charge: -4.000000
I can get to 256 lipids of pure POPC by also giving a (slightly higher) area per headgroup value with the -a flag, but it is less clear to me what the area should be in a mixed bilayer.
In short, my question is if there is a way to tell insane.py to generate a bilayer with a pre-determined number of lipids?
Thanks
/Per
I just discovered the very nice tool insane.py for constructing a martini cg-system from scratch, and have found it very easy to use.
I have however one question about how to make it generate a bilayer system with a given number of lipids in each leaflet.
From the help-text, it says that "if -d is omitted, those numbers are interpreted as absolute numbers", referencing the number of lipids in either leaflet I assume.
I have then tried both of the following, but I can't make the script produce a bilayer with the lipid composition and number of lipids that I want. I need a bilayer with 256 lipids in each leaflet, consisting of 75% POPC and 25% POPG. My command lines have been the following:
$ ./insane.py -o membrane_cg.gro -p membrane_cg.top -pbc cubic -box 13.78,14.27,11.11 -l POPC:192 -l POPG:64
This results in the output:
; X: 13.780 (18 lipids) Y: 14.270 (18 lipids)
; 324 lipids in upper leaflet, 324 lipids in lower leaflet
; Charge of membrane: -162.000000
; Total charge: -162.000000
So 324 lipids per leaflet in total, not 256. I assume it is no coincidence that 18*18=324 as well...
I prefer a cubic box, and my box-dimensions are from an atomistic system with the same constituents that I have already run.
I have also tried to take out all references to the box-size by running.
$ ./insane.py -o membrane_cg.gro -p membrane_cg.top -pbc cubic -l POPC:192 -l POPG:64
That gives the output:
; X: 2.500 (3 lipids) Y: 2.500 (3 lipids)
; 9 lipids in upper leaflet, 9 lipids in lower leaflet
; Charge of membrane: -4.000000
; Total charge: -4.000000
I can get to 256 lipids of pure POPC by also giving a (slightly higher) area per headgroup value with the -a flag, but it is less clear to me what the area should be in a mixed bilayer.
In short, my question is if there is a way to tell insane.py to generate a bilayer with a pre-determined number of lipids?
Thanks
/Per
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- xavier
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10 years 9 months ago #1799
by xavier
Replied by xavier on topic Using insane.py
Have you tried to specify the size and ratio of the two lipids instead of the exact numbers?
Not that the starting box size is not an issue. You will need to let it relax!
Not that the starting box size is not an issue. You will need to let it relax!
pela3247 wrote: Hi all,
I just discovered the very nice tool insane.py for constructing a martini cg-system from scratch, and have found it very easy to use.
I have however one question about how to make it generate a bilayer system with a given number of lipids in each leaflet.
From the help-text, it says that "if -d is omitted, those numbers are interpreted as absolute numbers", referencing the number of lipids in either leaflet I assume.
I have then tried both of the following, but I can't make the script produce a bilayer with the lipid composition and number of lipids that I want. I need a bilayer with 256 lipids in each leaflet, consisting of 75% POPC and 25% POPG. My command lines have been the following:
$ ./insane.py -o membrane_cg.gro -p membrane_cg.top -pbc cubic -box 13.78,14.27,11.11 -l POPC:192 -l POPG:64
This results in the output:
; X: 13.780 (18 lipids) Y: 14.270 (18 lipids)
; 324 lipids in upper leaflet, 324 lipids in lower leaflet
; Charge of membrane: -162.000000
; Total charge: -162.000000
So 324 lipids per leaflet in total, not 256. I assume it is no coincidence that 18*18=324 as well...
I prefer a cubic box, and my box-dimensions are from an atomistic system with the same constituents that I have already run.
I have also tried to take out all references to the box-size by running.
$ ./insane.py -o membrane_cg.gro -p membrane_cg.top -pbc cubic -l POPC:192 -l POPG:64
That gives the output:
; X: 2.500 (3 lipids) Y: 2.500 (3 lipids)
; 9 lipids in upper leaflet, 9 lipids in lower leaflet
; Charge of membrane: -4.000000
; Total charge: -4.000000
I can get to 256 lipids of pure POPC by also giving a (slightly higher) area per headgroup value with the -a flag, but it is less clear to me what the area should be in a mixed bilayer.
In short, my question is if there is a way to tell insane.py to generate a bilayer with a pre-determined number of lipids?
Thanks
/Per
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- pela3247
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10 years 9 months ago #1800
by pela3247
Replied by pela3247 on topic Using insane.py
Hi Xavier
Thanks for your reply. How exactly do I specify the size of each lipid?
Relative abundance I guess can be done like so:
./insane.py -f -o -p -l POPC:0.75 -l POPG:0.25
but that unfortunately still leaves me wondering how I should combine any of the -pbc, -d, -dz, -x, -y, -z or -box options to get fixed number of lipids in a reasonably sized box (and of course it needs to relax a bit at first :-)
Thanks again for your help.
/Per
Thanks for your reply. How exactly do I specify the size of each lipid?
Relative abundance I guess can be done like so:
./insane.py -f -o -p -l POPC:0.75 -l POPG:0.25
but that unfortunately still leaves me wondering how I should combine any of the -pbc, -d, -dz, -x, -y, -z or -box options to get fixed number of lipids in a reasonably sized box (and of course it needs to relax a bit at first :-)
Thanks again for your help.
/Per
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- xavier
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10 years 9 months ago #1801
by xavier
Replied by xavier on topic Using insane.py
I am not sure how these size are used by insane but I would try to define the x/y size to get the expected number of lipids (256) and only specify the relative abundance of each as you indicate ...
pela3247 wrote: Hi Xavier
Thanks for your reply. How exactly do I specify the size of each lipid?
Relative abundance I guess can be done like so:
./insane.py -f -o -p -l POPC:0.75 -l POPG:0.25
but that unfortunately still leaves me wondering how I should combine any of the -pbc, -d, -dz, -x, -y, -z or -box options to get fixed number of lipids in a reasonably sized box (and of course it needs to relax a bit at first :-)
Thanks again for your help.
/Per
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10 years 9 months ago #1820
by tsjerk
Replied by tsjerk on topic Using insane.py
Hey :)
There's an option -a to set the area per lipid. You can use that with the option -d to control the number of lipids. Unfortunately, it's not yet possible to specify exact numbers, despite the text in the help. That reflects what I really need to implement :S Sorry about that.
Cheers,
Tsjerk
There's an option -a to set the area per lipid. You can use that with the option -d to control the number of lipids. Unfortunately, it's not yet possible to specify exact numbers, despite the text in the help. That reflects what I really need to implement :S Sorry about that.
Cheers,
Tsjerk
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