The PLUMED CODE
PLUMED is a community-developed code that can be used to incorporate additional functionality into multiple molecular dynamics codes and for analysing trajectories. PLUMED is a composed of a modules that contain a variety of different functionalities but that share a common basic syntax. You can find a list of the modules that are available within PLUMED in the following graph. The graph also shows the interdependencies between the various modules. If you click on the modules in the graph module-specific information will open. The colors of the nodes in the graph below indicate whether the module is always compiled (blue), on by default (green) or off by default (red). If you need a feature from a module that is by default off you need to explicitly tell PLUMED to include it during the configure stage by using:
./configure --enable-module=module-name
Each module contains implementations of a number of actions. You can find a list of all the actions implemented in in PLUMED here.
Please also note that some developers prefer not to include their codes in PLUMED. To use functionality that has been written by these developed you can use the LOAD command.
If you are completely unfamiliar with PLUMED we would recommend that you start by working through the following tutorial.
%%{init: {"flowchart": {"defaultRenderer": "elk"}} }%%
flowchart TD
subgraph g0 [ ]
0("bias")
style 0 fill:green
1("generic")
style 1 fill:green
4("secondarystructure")
style 4 fill:green
6("annfunc")
style 6 fill:red
0~~~6;
38("pytorch")
style 38 fill:red
1~~~38;
end
11("function")
style 11 fill:green
11--> g0;
subgraph g2 [ ]
2("mapping")
style 2 fill:red
37("piv")
style 37 fill:red
39("s2cm")
style 39 fill:red
41("sizeshape")
style 41 fill:red
2~~~41;
17("landmarks")
style 17 fill:red
37~~~17;
31("membranefusion")
style 31 fill:red
39~~~31;
end
5("colvar")
style 5 fill:green
5--> g2;
subgraph g3 [ ]
35("maze")
style 35 fill:red
3("multicolvar")
style 3 fill:green
30("funnel")
style 30 fill:red
15("isdb")
style 15 fill:green
35~~~15;
end
0("bias")
style 0 fill:green
0--> g3;
5("colvar")
style 5 fill:green
5--> g3;
subgraph g10 [ ]
32("pamm")
style 32 fill:red
10("symfunc")
style 10 fill:red
16("clusters")
style 16 fill:red
19("gridtools")
style 19 fill:green
32~~~19;
27("envsim")
style 27 fill:red
10~~~27;
end
3("multicolvar")
style 3 fill:green
3--> g10;
14("adjmat")
style 14 fill:red
14--> g10;
subgraph g12 [ ]
34("logmfd")
style 34 fill:red
12("ves")
style 12 fill:red
24("drr")
style 24 fill:red
25("opes")
style 25 fill:red
34~~~25;
26("eds")
style 26 fill:red
12~~~26;
28("fisst")
style 28 fill:red
24~~~28;
end
0("bias")
style 0 fill:green
0--> g12;
subgraph g22 [ ]
43("wham")
style 43 fill:red
29("fourier")
style 29 fill:red
22("contour")
style 22 fill:red
end
19("gridtools")
style 19 fill:green
19--> g22;
subgraph g33 [ ]
40("sasa")
style 40 fill:red
33("setup")
style 33 fill:green
36("metatensor")
style 36 fill:red
end
23("core")
style 23 fill:blue
23--> g33;
0("bias")
style 0 fill:green
1("generic")
style 1 fill:green
1-->7;
1-->8;
1-->18;
1-->20;
2("mapping")
style 2 fill:red
2-->9;
3("multicolvar")
style 3 fill:green
4("secondarystructure")
style 4 fill:green
5("colvar")
style 5 fill:green
5-->7;
5-->13;
6("annfunc")
style 6 fill:red
7("vatom")
style 7 fill:green
7-->5;
8("volumes")
style 8 fill:red
9("dimred")
style 9 fill:red
10("symfunc")
style 10 fill:red
11("function")
style 11 fill:green
12("ves")
style 12 fill:red
13("crystdistrib")
style 13 fill:red
14("adjmat")
style 14 fill:red
14-->13;
14-->42;
15("isdb")
style 15 fill:green
16("clusters")
style 16 fill:red
17("landmarks")
style 17 fill:red
17-->9;
18("valtools")
style 18 fill:blue
18-->11;
18-->20;
19("gridtools")
style 19 fill:green
19-->9;
20("matrixtools")
style 20 fill:green
20-->14;
20-->21;
21("refdist")
style 21 fill:green
21-->5;
22("contour")
style 22 fill:red
23("core")
style 23 fill:blue
23-->11;
23-->18;
24("drr")
style 24 fill:red
25("opes")
style 25 fill:red
26("eds")
style 26 fill:red
27("envsim")
style 27 fill:red
28("fisst")
style 28 fill:red
29("fourier")
style 29 fill:red
30("funnel")
style 30 fill:red
31("membranefusion")
style 31 fill:red
32("pamm")
style 32 fill:red
33("setup")
style 33 fill:green
34("logmfd")
style 34 fill:red
35("maze")
style 35 fill:red
36("metatensor")
style 36 fill:red
37("piv")
style 37 fill:red
38("pytorch")
style 38 fill:red
39("s2cm")
style 39 fill:red
40("sasa")
style 40 fill:red
41("sizeshape")
style 41 fill:red
42("sprint")
style 42 fill:red
43("wham")
style 43 fill:red
click 0 "bias.html" "Information about the module [Authors: list of authors]"
click 1 "generic.html" "Information about the module [Authors: list of authors]"
click 2 "mapping.html" "Information about the module [Authors: list of authors]"
click 3 "multicolvar.html" "Information about the module [Authors: list of authors]"
click 4 "secondarystructure.html" "Information about the module [Authors: list of authors]"
click 5 "colvar.html" "Information about the module [Authors: list of authors]"
click 6 "annfunc.html" "Information about the module [Authors: list of authors]"
click 7 "vatom.html" "Information about the module [Authors: list of authors]"
click 8 "volumes.html" "Information about the module [Authors: list of authors]"
click 9 "dimred.html" "Information about the module [Authors: list of authors]"
click 10 "symfunc.html" "Information about the module [Authors: list of authors]"
click 11 "function.html" "Information about the module [Authors: list of authors]"
click 12 "ves.html" "Information about the module [Authors: list of authors]"
click 13 "crystdistrib.html" "Information about the module [Authors: list of authors]"
click 14 "adjmat.html" "Information about the module [Authors: list of authors]"
click 15 "isdb.html" "Information about the module [Authors: list of authors]"
click 16 "clusters.html" "Information about the module [Authors: list of authors]"
click 17 "landmarks.html" "Information about the module [Authors: list of authors]"
click 18 "valtools.html" "Information about the module [Authors: list of authors]"
click 19 "gridtools.html" "Information about the module [Authors: list of authors]"
click 20 "matrixtools.html" "Information about the module [Authors: list of authors]"
click 21 "refdist.html" "Information about the module [Authors: list of authors]"
click 22 "contour.html" "Information about the module [Authors: list of authors]"
click 23 "core.html" "Information about the module [Authors: list of authors]"
click 24 "drr.html" "Information about the module [Authors: list of authors]"
click 25 "opes.html" "Information about the module [Authors: list of authors]"
click 26 "eds.html" "Information about the module [Authors: list of authors]"
click 27 "envsim.html" "Information about the module [Authors: list of authors]"
click 28 "fisst.html" "Information about the module [Authors: list of authors]"
click 29 "fourier.html" "Information about the module [Authors: list of authors]"
click 30 "funnel.html" "Information about the module [Authors: list of authors]"
click 31 "membranefusion.html" "Information about the module [Authors: list of authors]"
click 32 "pamm.html" "Information about the module [Authors: list of authors]"
click 33 "setup.html" "Information about the module [Authors: list of authors]"
click 34 "logmfd.html" "Information about the module [Authors: list of authors]"
click 35 "maze.html" "Information about the module [Authors: list of authors]"
click 36 "metatensor.html" "Information about the module [Authors: list of authors]"
click 37 "piv.html" "Information about the module [Authors: list of authors]"
click 38 "pytorch.html" "Information about the module [Authors: list of authors]"
click 39 "s2cm.html" "Information about the module [Authors: list of authors]"
click 40 "sasa.html" "Information about the module [Authors: list of authors]"
click 41 "sizeshape.html" "Information about the module [Authors: list of authors]"
click 42 "sprint.html" "Information about the module [Authors: list of authors]"
click 43 "wham.html" "Information about the module [Authors: list of authors]"