Order parameters for individual leaflets
gorder can calculate order parameters for the entire membrane as well as for the individual leaflets.
To do this, you need to specify a method for classifying lipids into membrane leaflets. By default, gorder assigns lipids to membrane leaflets independently for each analyzed frame (this can be customized, see Classification frequency), making it suitable even for the analysis of membranes where lipids flip-flop between leaflets.
There are three leaflet classification methods available in gorder: global, local, and individual. In case you are not satisfied with any of them, you can also assign lipids into leaflets manually.
When calculating order parameters for vesicles or similar highly curved membranes, you should always assign lipids into leaflets manually.
Global method for leaflet classification
Fast and reliable. Recommended for most membranes.
In this method, lipid molecules are assigned to membrane leaflets based on the position of their 'head identifier' relative to the global membrane center of geometry. The 'head identifier' is a single atom representing the head of the lipid. If the 'head identifier' is located "above" the membrane center, the lipid is assigned to the upper leaflet; if it is located "below", it is assigned to the lower leaflet.
To use this method, you must specify the 'head identifier' atoms and all atoms that form the membrane. GSL is used to define these selections.
leaflets: !Global
membrane: "@membrane"
heads: "name P"
Here, we use autodetected membrane atoms to calculate the membrane center and select atoms named 'P' (phosphorus atoms of lipids) as head identifiers. Each analyzed lipid must have exactly one head identifier atom; otherwise, an error will occur.
Local method for leaflet classification
Slow but reliable. Useful for some slightly curved systems.
In this method, lipid molecules are assigned to membrane leaflets based on the position of their 'head identifier' relative to the local membrane center of geometry. The local membrane center is calculated using atoms in a cylinder around the 'head identifier'. If the 'head identifier' is located "above" the local center, the lipid is assigned to the upper leaflet; if "below", it is assigned to the lower leaflet.
For this method, you need to specify a selection of head identifiers, all atoms forming the membrane, and the radius of the cylinder used to define the local membrane.
leaflets: !Local
membrane: "@membrane"
heads: "name P"
radius: 2.5
Autodetected membrane atoms will be used to calculate the membrane center. Only atoms within a cylinder of radius 2.5 nm (with infinite height) centered on the 'head identifier' and oriented along the membrane normal will be used for the local center calculation. The atoms named 'P' (phosphorus atoms of lipids) are used as 'head identifiers'.
Individual method for leaflet classification
Very fast but less reliable. Recommended for very large membranes.
In this method, lipid molecules are assigned to membrane leaflets based on the position of their 'head identifier' relative to their 'tail ends'. 'Tail ends' refer to the last heavy atoms or beads of the lipid tails. Each lipid molecule may have multiple 'tail ends', but only one 'head identifier'. If the 'head identifier' is located "above" the 'tail ends', the lipid is assigned to the upper leaflet; if it is located "below", it is assigned to the lower leaflet.
To use this method, you must specify selections for the 'head identifiers' and the 'tail ends'.
leaflets: !Individual
heads: "name P"
methyls: "name C218 C316"
In this example, atoms named 'P' (phosphorus atoms of lipids) are used as head identifiers, and 'C218' or 'C316' atoms (the last carbons of oleoyl and palmitoyl chains) are used as tail ends.
Classification frequency
By default, gorder performs leaflet classification independently for each analyzed frame. This ensures accurate analysis in membranes where lipid exchange occurs between leaflets. However, you can modify this behavior using the frequency keyword to specify how often leaflet classification should be performed.
Once
If you know that lipid flip-flop does not occur in your system and want to accelerate the analysis, you can use frequency: !Once. This option assigns lipids to individual membrane leaflets based on the first trajectory frame (not the TPR file structure), and this assignment is then used for all subsequent trajectory frames.
Example usage:
leaflets: !Local
membrane: "@membrane"
heads: "name P"
radius: 2.5
frequency: !Once
Using
frequency: !Onceis especially useful for the Local classification method which is very computationally expensive.
Every N frames
Alternatively, you can specify that classification should occur every N analyzed trajectory frames using frequency: !Every N. For example, frequency: !Every 10 means that classification will be performed every 10 analyzed trajectory frames, with the closest previous assignment used for intermediate frames.
Example usage:
leaflets: !Global
membrane: "@membrane"
heads: "name P"
frequency: !Every 10
Important note: The frequency applies to analyzed trajectory frames. For instance, if the classification frequency is set to 10 and the analysis step size is 5 (see Analyzing a part of the trajectory), leaflet classification will occur every 50th (10×5) frame in the input trajectory.
Membrane normal
All leaflet classification methods use the specified membrane normal to determine what is 'up' and what is 'down'. If your membrane is planar and aligned with the xy plane, no further action is needed. Otherwise, refer to this section of the manual.
Here, we just mention that the membrane normal used for leaflet classification can be decoupled from the 'global' membrane normal used for calculating order parameters:
leaflets: !Global
membrane: "@membrane"
heads: "name P"
membrane_normal: x # used only for leaflet classification
Leaflet-wise output
When a leaflet classification method is defined, gorder calculates order parameters for both the entire membrane and individual leaflets. Leaflet-specific order parameters are included in all gorder output formats: YAML, CSV, "table", and XVG.
During analysis, gorder also prints information about membrane composition in the first trajectory frame, allowing you to quickly check for any obvious errors. Such membrane composition information may look like this:
(...)
[*] Upper leaflet in the first analyzed frame: POPE: 45, POPC: 50, POPG: 5
[*] Lower leaflet in the first analyzed frame: POPE: 45, POPC: 50, POPG: 5
(...)
Below is an excerpt from an output YAML file containing results for individual membrane leaflets:
# Order parameters calculated with 'gorder v0.6.0' using a structure file 'system.tpr' and a trajectory file 'md.xtc'.
average order:
total: 0.1631
upper: 0.1629
lower: 0.1632
POPE:
average order:
total: 0.1601
upper: 0.1603
lower: 0.1598
order parameters:
POPE C22 (23):
total: 0.1036
upper: 0.1069
lower: 0.1003
bonds:
POPE H2R (24):
total: 0.0876
upper: 0.0924
lower: 0.0828
POPE H2S (25):
total: 0.1196
upper: 0.1214
lower: 0.1178
POPE C32 (32):
total: 0.2297
upper: 0.2291
lower: 0.2303
bonds:
POPE H2X (33):
total: 0.2423
upper: 0.241
lower: 0.2437
POPE H2Y (34):
total: 0.2171
upper: 0.2173
lower: 0.2168
#(...)
POPC:
average order:
total: 0.166
upper: 0.1654
lower: 0.1665
order parameters:
POPC C22 (32):
total: 0.1109
upper: 0.1117
lower: 0.1101
bonds:
POPC H2R (33):
total: 0.0935
upper: 0.0966
lower: 0.0904
POPC H2S (34):
total: 0.1283
upper: 0.1268
lower: 0.1297
POPC C32 (41):
total: 0.2373
upper: 0.236
lower: 0.2387
bonds:
POPC H2X (42):
total: 0.2483
upper: 0.2446
lower: 0.2519
POPC H2Y (43):
total: 0.2264
upper: 0.2273
lower: 0.2255
#(...)
POPG:
average order:
total: 0.1608
upper: 0.1621
lower: 0.1594
order parameters:
POPG C22 (25):
total: 0.0987
upper: 0.103
lower: 0.0944
bonds:
POPG H2R (26):
total: 0.08
upper: 0.0841
lower: 0.0759
POPG H2S (27):
total: 0.1174
upper: 0.1219
lower: 0.1129
POPG C32 (34):
total: 0.2272
upper: 0.2293
lower: 0.2251
bonds:
POPG H2X (35):
total: 0.2367
upper: 0.2391
lower: 0.2342
POPG H2Y (36):
total: 0.2177
upper: 0.2195
lower: 0.2159
#(...)