The system is a bilayer of 880 POPC molecules. 480 POPC molecules are restrained, enforcing a positive curvature (designated in the structure file as 'POPP'), the rest are free to move.
I am including my structure file, short trajectory of three frames, screnshot of the settings and a file with the total area showing, that the program doesn't select the same number of lipids for each leaflet every time.
After analyzing the problem a bit I see two different issues here.
1) The system present significant curvature
That makes the selection method of which lipids are in the upper and lower leafleat to fail. I think that this is a know problem of our sofware and we should probably warn the users better.
** 2) The calculation of the total area per lipid fails**
While the are per lipid (POPC) look correct, they are small because of the curvature, the issue is that the total is a mess. At this point, I do not understand the numbers.
Last edit: Hector Martinez-Seara Monne 2018-10-29
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For obtaining the number of lipids in the system and indentifying which residues are in the upper and lower leaflet, the internal VMD property "residue" is used. This property identifies residues automatically using connectivity.
In this specific case, VMD has failed to guess connectivity creating hundreds of fragments with individual "residue" numbers.
Total area per lipid = Total area / number of lipids in the system
Hence, the mess in the Total area per lipid is caused by unreliable connectivity definition.
To solve this issue, please generate a PSF file and use it instead of the GRO file.
More info at General Requirements.
The system is a bilayer of 880 POPC molecules. 480 POPC molecules are restrained, enforcing a positive curvature (designated in the structure file as 'POPP'), the rest are free to move.
I am including my structure file, short trajectory of three frames, screnshot of the settings and a file with the total area showing, that the program doesn't select the same number of lipids for each leaflet every time.
Last edit: daniel holy 2018-10-29
After analyzing the problem a bit I see two different issues here.
1) The system present significant curvature
That makes the selection method of which lipids are in the upper and lower leafleat to fail. I think that this is a know problem of our sofware and we should probably warn the users better.
** 2) The calculation of the total area per lipid fails**
While the are per lipid (POPC) look correct, they are small because of the curvature, the issue is that the total is a mess. At this point, I do not understand the numbers.
Last edit: Hector Martinez-Seara Monne 2018-10-29
Updated wiki to add in requeriments that extremly deformed membranes may lead to leaflet assignment issues.
Last edit: Ismael Rodriguez Espigares 2018-11-12
For obtaining the number of lipids in the system and indentifying which residues are in the upper and lower leaflet, the internal VMD property "residue" is used. This property identifies residues automatically using connectivity.
In this specific case, VMD has failed to guess connectivity creating hundreds of fragments with individual "residue" numbers.
Total area per lipid = Total area / number of lipids in the system
Hence, the mess in the Total area per lipid is caused by unreliable connectivity definition.
To solve this issue, please generate a PSF file and use it instead of the GRO file.
More info at General Requirements.
Related
Wiki: GeneralRequirements