6.7. geom with CHARMM
There is an internally-integrated CHARMM force field calculation engine in geom, enabling global optimization of organic and bio-organic molecular clusters. This can be done easily as long as you have CHARMM parameter files and PSF topology files for your system.
To call internally-integrated CHARMM, you should use the following input:
geom.inp
1components
2 a.xyz 10
3 random 0 0 0 5 5 5
4 ****
5 b.xyz 20
6 random 0 0 0 5 5 5
7 ****
8end
9charmm
10 parameter.inp
11 a.psf
12 b.psf
13end
14commands
15 $charmm$
16end
In charmm block, you should input a parameter file name (path included if necessary) followed by PSF files for each component defined in components block.
Note that when charmm block is present, generated clusters will also be saved in PDB format. A PSF file for the whole cluster named X.psf will also be generated.
6.7.1. Example: Decaalanines
Tip
The sample input and output files can be found in testfiles/geom/8-aladeca-charmm.
In this Section we will see how to use geom to look for the stable configurations of some special shape of decaalanines.
The structure of decaalanine is:
deca-ala.pdb
1REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000
2ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH
3ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH
4ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH
5ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH
6ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH
7ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH
8ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH
9ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH
10ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH
11ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH
12ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH
13ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH
14ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH
15ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH
16ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH
17ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH
18ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH
19ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH
20ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH
21ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH
22ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH
23ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH
24ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH
25ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH
26ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH
27ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH
28ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH
29ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH
30ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH
31ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH
32ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH
33ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH
34ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH
35ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH
36ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH
37ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH
38ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH
39ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH
40ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH
41ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH
42ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH
43ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH
44ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH
45ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH
46ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH
47ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH
48ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH
49ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH
50ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH
51ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH
52ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH
53ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH
54ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH
55ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH
56ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH
57ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH
58ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH
59ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH
60ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH
61ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH
62ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH
63ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH
64ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH
65ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH
66ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH
67ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH
68ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH
69ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH
70ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH
71ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH
72ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH
73ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH
74ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH
75ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH
76ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH
77ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH
78ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH
79ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH
80ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH
81ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH
82ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH
83ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH
84ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH
85ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH
86ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH
87ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH
88ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH
89ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH
90ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH
91ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH
92ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH
93ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH
94ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH
95ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH
96ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH
97ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH
98ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH
99ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH
100ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH
101ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH
102ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH
103ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH
104ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH
105ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH
106END
To enable CHARMM calculations, a PSF file for this peptide and a CHARMM parameter file are needed: deca-ala.psf and par_all27_prot_lipid.prm.
6.7.1.1. Packing
We want to see what they will pack into. Let’s try 13 decaalanines. The input file is:
deca-ala-packing.inp
1lm_dir deca-ala-packing # Save the local minima to this folder.
2num_calcs 20 # Total number of calculations.
3do_coarse_opt yes # no: Do NOT the coarse optimization.
4min_energy_gap 1.E-5 # When two energies differ smaller than
5 # this value, they are treated as identical.
6 # A negative number means do not remove
7 # energetically degenerated ones.
8max_geom_iters 3000 # The maximum number of iterations for local optimization.
9 # If it is less or equal than zero, then the number is unlimited.
10use_CUDA yes # yes: Will always use CUDA when GPU acceleration is enabled.
11
12components
13 deca-ala.pdb 13
14 random 0 0 0 15 15 15
15 ****
16end
17
18charmm
19 par_all27_prot_lipid.prm
20 deca-ala.psf
21end
22
23commands
24 $charmm$
25end
You can see that, we use $charmm$ to enable internal CHARMM calculation engine, and random to put decaalanines in a box defined by (0, 0, 0) and (15, 15, 15).
Now you can run the global optimization:
$ geom deca-ala-packing.inp > deca-ala-packing.out
After the optimization, the end of deca-ala-packing.out is
deca-ala-packing.out
-- Result Report --
Results are energy-increasingly reordered.
Structures of energies within 1.000E-04 are treated as degenerate.
All minima are saved to "deca-ala-packing".
-------------------------------------------------------------------
# index Energy NaiveRMSD
-------------------------------------------------------------------
0 19 -4146.88610026 0.00000000
1 5 -4136.05019723 14.82412036
2 0 -4121.59161174 14.58105056
3 3 -4046.70846315 18.63580831
4 14 -4043.04825505 15.53391890
5 16 -4012.00784464 16.42782901
6 1 -4010.99019118 17.58161163
The global minimum of this system is deca-ala-packing/19.xyz, which is shown below:
Tip
In practice, use a large num_calcs to get more reliable results.
6.7.1.2. Layer
Let’s try to make a layer of 15 decaalanines. The input file is:
deca-ala-layer.inp
1lm_dir deca-ala-layer # Save the local minima to this folder.
2num_calcs 20 # Total number of calculations.
3do_coarse_opt yes # no: Do NOT the coarse optimization.
4min_energy_gap 1.E-5 # When two energies differ smaller than
5 # this value, they are treated as identical.
6 # A negative number means do not remove
7 # energetically degenerated ones.
8max_geom_iters 3000 # The maximum number of iterations for local optimization.
9 # If it is less or equal than zero, then the number is unlimited.
10use_CUDA yes # yes: Will always use CUDA when GPU acceleration is enabled.
11
12components
13 deca-ala.pdb 15
14 layer 1 4 99 0 0 1 30 0 0 0 30 0 30 30 0
15 ****
16end
17
18charmm
19 par_all27_prot_lipid.prm
20 deca-ala.psf
21end
22
23commands
24 $charmm$
25end
We use layer to put decaalanines in a layer of (30, 0, 0), (0, 30, 0), and (30, 30, 0). 4 99 means that atom 4 is closer to the layer, and 4 99 points along the local normal (0, 0, 1),. The first 1 means they are distributed regularly.
Now you can run the global optimization:
$ geom deca-ala-layer.inp > deca-ala-layer.out
After the optimization, the end of deca-ala-layer.out is
deca-ala-layer.out
-- Result Report --
Results are energy-increasingly reordered.
Structures of energies within 1.000E-04 are treated as degenerate.
All minima are saved to "deca-ala-layer".
-------------------------------------------------------------------
# index Energy NaiveRMSD
-------------------------------------------------------------------
0 7 -4652.84360462 0.00000000
1 10 -4642.74868570 6.95594683
2 9 -4640.17531448 5.49849160
3 17 -4620.62326625 5.27290071
4 6 -4606.48231626 5.79743188
5 2 -4589.08824421 5.33432251
The global minimum of this system is deca-ala-layer/7.xyz, which is shown below:
