Output formats

The YAML output is always generated by gorder, as it contains all the calculated information. See Atomistic Order Parameters or Coarse-grained Order Parameters for more details about this format. However, gorder can also write output in other formats.

CSV format

CSV format may be useful if you want to work with the results using spreadsheet software such as LibreOffice Calc or Microsoft Excel, or when working with data analysis libraries like Pandas or Polars.

To write the results of the analysis in CSV format, add output_csv: PATH_TO_OUTPUT to your input YAML file.

Here is an excerpt from a CSV file:

molecule,residue,atom,relative index,total,hydrogen #1,hydrogen #2,hydrogen #3
POPE,POPE,C22,23,0.1098,0.0946,0.1250,
POPE,POPE,C32,32,0.2341,0.2438,0.2244,
POPE,POPE,C23,35,0.2172,0.2168,0.2175,
POPE,POPE,C24,38,0.2214,0.2193,0.2235,
POPE,POPE,C25,41,0.2333,0.2341,0.2325,
POPE,POPE,C26,44,0.2137,0.2144,0.2129,
POPE,POPE,C27,47,0.2040,0.2036,0.2044,
POPE,POPE,C28,50,0.1206,0.1193,0.1220,
POPE,POPE,C29,53,0.0748,0.0748,,
POPE,POPE,C210,55,0.0600,0.0600,,
(...)
POPE,POPE,C218,78,0.0324,0.0329,0.0321,0.0322
(...)
POPC,POPC,C22,32,0.1094,0.0953,0.1235,
POPC,POPC,C32,41,0.2325,0.2405,0.2245,
POPC,POPC,C23,44,0.2228,0.2232,0.2224,
POPC,POPC,C24,47,0.2228,0.2228,0.2228,
POPC,POPC,C25,50,0.2356,0.2366,0.2347,
POPC,POPC,C26,53,0.2150,0.2165,0.2134,
POPC,POPC,C27,56,0.2058,0.2055,0.2062,
POPC,POPC,C28,59,0.1220,0.1239,0.1201,
POPC,POPC,C29,62,0.0712,0.0712,,
POPC,POPC,C210,64,0.0648,0.0648,,
(...)
POPC,POPC,C218,87,0.0344,0.0351,0.0340,0.0341
(...)
POPG,POPG,C22,25,0.1081,0.1024,0.1138,
POPG,POPG,C32,34,0.2028,0.2131,0.1926,
POPG,POPG,C23,37,0.2107,0.2172,0.2041,
POPG,POPG,C24,40,0.2170,0.2189,0.2151,
POPG,POPG,C25,43,0.2367,0.2341,0.2392,
POPG,POPG,C26,46,0.2193,0.2191,0.2195,
POPG,POPG,C27,49,0.2101,0.2094,0.2108,
POPG,POPG,C28,52,0.1233,0.1181,0.1286,
POPG,POPG,C29,55,0.0806,0.0806,,
POPG,POPG,C210,57,0.0597,0.0597,,
(...)
POPG,POPG,C218,80,0.0351,0.0361,0.0345,0.0346

Each line corresponds to one heavy atom type (or one bond type in the case of coarse-grained systems). The first column corresponds to the molecule name, the second to the residue name, the third to the atom name, the fourth to the relative index of the atom type, the fifth to the order parameter calculated for this atom type, and the following columns correspond to the order parameters of the bonds the heavy atom type is involved in.

Table format

The Table format presents the results of the analysis in a clear, human-readable format.

To write the results of the analysis in Table format, add output_tab: PATH_TO_OUTPUT to your input YAML file.

Here is an excerpt from a Table file:

# Order parameters calculated with 'gorder v0.2.0' using structure file 'system.tpr' and trajectory file 'md.xtc'.

Molecule type POPE
           TOTAL   |   H #1   |   H #2   |   H #3   |
C22        0.1098  |  0.0946  |  0.1250  |          |
C32        0.2341  |  0.2438  |  0.2244  |          |
C23        0.2172  |  0.2168  |  0.2175  |          |
C24        0.2214  |  0.2193  |  0.2235  |          |
(...)

Molecule type POPC
           TOTAL   |   H #1   |   H #2   |   H #3   |
C22        0.1094  |  0.0953  |  0.1235  |          |
C32        0.2325  |  0.2405  |  0.2245  |          |
C23        0.2228  |  0.2232  |  0.2224  |          |
C24        0.2228  |  0.2228  |  0.2228  |          |
(...)

Molecule type POPG
           TOTAL   |   H #1   |   H #2   |   H #3   |
C22        0.1081  |  0.1024  |  0.1138  |          |
C32        0.2028  |  0.2131  |  0.1926  |          |
C23        0.2107  |  0.2172  |  0.2041  |          |
C24        0.2170  |  0.2189  |  0.2151  |          |
(...)

Each line corresponds to one heavy atom type (or one bond type in the case of coarse-grained systems). The first column corresponds to the name of the atom type, the second to the order parameter calculated for this atom type, and the following columns correspond to the order parameters of the bond the heavy atom type is involved in.

XVG format

XVG format may be useful if you want to quickly visualize the results as plots using xmgrace.

To write the results of the analysis in XVG format, add output_xvg: FILE_PATTERN to your input YAML file. One XVG file will be created for each molecule. The name of the molecule will be appended to the end of the file stem. For example, if your file pattern is order.xvg and the membrane contains POPC, POPE, and POPG lipid molecules, three XVG files will be generated: order_POPC.xvg, order_POPE.xvg, and order_POPG.xvg.

Here is an excerpt from an XVG file:

# Order parameters calculated with 'gorder v0.2.0' using structure file 'system.tpr' and trajectory file 'md.xtc'.
@    title "Atomistic order parameters for molecule type POPC"
@    xaxis label "Atom"
@    yaxis label "-Sch"
@    s0 legend "Full membrane"
@TYPE xy
# Atom C22:
1      0.1094 
# Atom C32:
2      0.2325 
# Atom C23:
3      0.2228 
# Atom C24:
4      0.2228 
# Atom C25:
5      0.2356 
# Atom C26:
6      0.2150 
# Atom C27:
7      0.2058 
# Atom C28:
8      0.1220 
(...)

XVG files provide the least complete information. The first column is the index of the analyzed heavy atom type (starting from 1), and the second column is the order parameter of the atom type.

Example of an input YAML file with all supported outputs requested

structure: system.tpr
trajectory: md.xtc
analysis_type: !AAOrder
  heavy_atoms: "@membrane and name r'C3([2-9]|1[0-6])|C2([2-9]|1[0-8])'"
  hydrogens: "@membrane and element name hydrogen"
output_yaml: order.yaml    # for yaml format, you can use either `output` or `output_yaml`
output_tab: order.tab
output_xvg: order.xvg
output_csv: order.csv