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83
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT Normal file
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###########################################################
# Interaction of a carbon nanotube with a pair of "mystery
# molecules" (extracted from the cnat-cnt.data/in files).
###########################################################
# Author: Aysun Itai and Andrew Jewett
This example uses "ltemplify.py" to create molecule templates out
of two different molecules in a pre-existing LAMMPS IN/DATA file.
Then I show how to use "moltemplate.sh" to make copies of these
molecules and to move and rotate them (creating new LAMMPS IN/DATA files).
Disclaimer:
The molecules in this example are not physically realistic.
The purpose of this example is to demonstrate ltemplify usage.
REQUIRED INPUT FILES
cnad-cnt.data cnad-cnt.in system.lt
cnad-cnt.data
This is a LAMMPS data file containing the coordinates and the topology
for a system combining the two molecules together. ltemplify will extract
molecules from this file, one at a time.
cnad-cnt.in
This file contains force-field parameters and old run settings for the system.
(We ignore the run settings in this file.) The force-field parameters in
the "cnad-cnt.in" file are only necessary because we are going to build
a completely new set of simulation input files. (We are not only going to
rotate them and duplicate the molecules.) ltemplify.py will extract the
force field parameters from this file. This approach allows us to combine
these molecules with other types of molecules later on.)
system.lt
The "system.lt" contains the instructions what we will do with these molecules
after ltemplify.py has converted them into .LT format. In this example
it contains instructions for rotating and copying the two molecules,
(It also defines the periodic boundary conditions.)
OUTPUT FILES
cnad.lt
cnt.lt
These files are referenced in system.lt.
Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt")
creates new LAMMPS data and input files:
system.data, system.in, system.in.init, system.in.settings
(These files are referenced in run.in.nvt.)
You can run a simulation from the files created by moltemplate using
lmp_linux -i run.in.nvt
NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY
ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED.
(This was done to protect the original source of the files.)
The goal of this example is only to demonstrate how to use
"ltemplify.py" to convert lammps input and data files into
LT format and back again.)
-----------
Instructions:
Run the commands (follow the instructions) in these files:
step 1)
README_step1_run_ltemplify.sh
and then
step 2)
README_step2_run_moltemplate.sh
step 3) OPTIONAL
To run a short LAMMPS simulation, you can use the "in.nvt" file, for example:
$LAMMPS_BINARY -i run.in.nvt
where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...).
-----------

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tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh Executable file
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#!/bin/sh
# Aysun Itai's LAMMPS files contain two molecules:
# The CNAD molecule has molecule-id 1
ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt
# The CNT (carbon nanotube) corresponds to molecule-id 2
ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt
# This will extract both molecules and save them as separate .LT files.
# (We can include these files later when preparing new simulations.)

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tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh Executable file
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# --- Running Moltemplate ---
# -- Prerequisites: --
# The "system.lt" moltemplate file links to other ".lt" files
# files you hopefully have created earlier when you ran "ltemplify.py:
# cnad.lt and cnt.lt
# If not, carry out the instructions in "README_run_ltemplify.sh".
moltemplate.sh system.lt
# This will generate various files with names ending in *.in* and *.data.
# These files are the input files directly read by LAMMPS.
# Optional:
# The "./output_ttree/" directory is full of temporary files generated by
# moltemplate. They can be useful for debugging, but are usually thrown away.
rm -rf output_ttree/

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tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh Executable file
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# --- Running LAMMPS ---
# -- Prerequisites: --
# The "run.in.nvt" LAMMPS input script links to the input
# scripts and data files you hopefully have created earlier
# with moltemplate.sh:
# system.in.init, system.in.settings, system.data
# If not, carry out the instructions in "README_run_moltemplate.sh".
#
# -- Instructions: --
# If "lmp_linux" is the name of the command you use to invoke lammps,
# then you would run lammps this way:
lmp_linux -i run.in.nvt
# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY
# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY.

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tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt Normal file
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------- To view the trajectory in VMD --------
1) Build a PSF file for use in viewing with VMD.
This step works with VMD 1.9 and topotools 1.2.
(Older versions, like VMD 1.8.6, don't support this.)
a) Start VMD
b) Menu Extensions->Tk Console
c) Enter:
(I assume that the the DATA file is called "system.data")
topo readlammpsdata system.data full
animate write psf system.psf
Later, to Load a trajectory in VMD:
Start VMD
Select menu: File->New Molecule
-Browse to select the PSF file you created above, and load it.
(Don't close the window yet.)
-Browse to select the trajectory file.
If necessary, for "file type" select: "LAMMPS Trajectory"
Load it
----- Wrap the coordinates to the unit cell
a) Start VMD
b) Load the trajectory in VMD (see above)
c) Menu Extensions->Tk Console
d) Enter:
DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT.
LOOKUP "pbctools" FOR DETAILS.
pbc wrap -compound res -all
pbc box
3) Optional: If you like, change the atom types in the PSF file so
that VMD recognizes the atom types, use something like:
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
(If you do this, it might effect step 2 above.)

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#Created by Aysun Itai and modified by Andrew Jewett
# NOTE: This file has been extensively modified.
# Only the bond connectivity and atomic positions are accurate.
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
pair_style lj/charmm/coul/charmm 8.0 10.0
pair_modify mix arithmetic
read_data cnad-cnt.data
pair_coeff 1 1 0.02 4.0
pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically
pair_coeff 3 3 0.02 2.0 # in this version of the file.
pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed)
pair_coeff 5 5 0.02 2.0
pair_coeff 6 6 0.02 3.0
pair_coeff 7 7 0.02 3.0
pair_coeff 8 8 0.02 3.0
pair_coeff 9 9 0.02 4.0
pair_coeff 10 10 0.02 4.0
pair_coeff 11 11 0.02 4.0
pair_coeff 12 12 0.02 4.0
pair_coeff 13 13 0.02 3.0
pair_coeff 14 14 0.02 3.0
pair_coeff 15 15 0.02 3.0
pair_coeff 16 16 0.02 3.0
group cnt type 1
group cnad type 2-16
displace_atoms cnad move 0 -7 0 units box
special_bonds charmm
velocity all create 0.0 54321 dist uniform
thermo 1
thermo_style multi
timestep 0.005
dump 1 all atom 10 cnad-cnt.dump
run 20000

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tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf Normal file
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PSF
1 !NTITLE
REMARKS VMD generated structure x-plor psf file
130 !NATOM
1 1 1 1 0.000000 10.0000 0
2 1 1 1 0.000000 10.0000 0
3 1 1 1 0.000000 10.0000 0
4 1 1 1 0.000000 10.0000 0
5 1 1 1 0.000000 10.0000 0
6 1 1 1 0.000000 10.0000 0
7 1 1 1 0.000000 10.0000 0
8 1 1 1 0.000000 10.0000 0
9 1 1 1 0.000000 10.0000 0
10 1 1 1 0.000000 10.0000 0
11 1 1 1 0.000000 10.0000 0
12 1 1 1 0.000000 10.0000 0
13 1 1 1 0.000000 10.0000 0
14 1 1 1 0.000000 10.0000 0
15 1 1 1 0.000000 10.0000 0
16 1 1 1 0.000000 10.0000 0
17 1 1 1 0.000000 10.0000 0
18 1 1 1 0.000000 10.0000 0
19 1 1 1 0.000000 10.0000 0
20 1 1 1 0.000000 10.0000 0
21 1 1 1 0.000000 10.0000 0
22 1 1 1 0.000000 10.0000 0
23 1 1 1 0.000000 10.0000 0
24 1 1 1 0.000000 10.0000 0
25 1 1 1 0.000000 10.0000 0
26 1 1 1 0.000000 10.0000 0
27 1 1 1 0.000000 10.0000 0
28 1 1 1 0.000000 10.0000 0
29 1 1 1 0.000000 10.0000 0
30 1 1 1 0.000000 10.0000 0
31 1 1 1 0.000000 10.0000 0
32 1 1 1 0.000000 10.0000 0
33 1 1 1 0.000000 10.0000 0
34 1 1 1 0.000000 10.0000 0
35 1 1 1 0.000000 10.0000 0
36 1 1 1 0.000000 10.0000 0
37 1 1 1 0.000000 10.0000 0
38 1 1 1 0.000000 10.0000 0
39 1 1 1 0.000000 10.0000 0
40 1 1 1 0.000000 10.0000 0
41 1 1 1 0.000000 10.0000 0
42 1 1 1 0.000000 10.0000 0
43 1 1 1 0.000000 10.0000 0
44 1 1 1 0.000000 10.0000 0
45 1 1 1 0.000000 10.0000 0
46 1 1 1 0.000000 10.0000 0
47 1 1 1 0.000000 10.0000 0
48 1 1 1 0.000000 10.0000 0
49 1 1 1 0.000000 10.0000 0
50 1 1 1 0.000000 10.0000 0
51 1 1 1 0.000000 10.0000 0
52 1 1 1 0.000000 10.0000 0
53 1 1 1 0.000000 10.0000 0
54 1 1 1 0.000000 10.0000 0
55 1 1 1 0.000000 10.0000 0
56 1 1 1 0.000000 10.0000 0
57 1 1 1 0.000000 10.0000 0
58 1 1 1 0.000000 10.0000 0
59 1 1 1 0.000000 10.0000 0
60 1 1 1 0.000000 10.0000 0
61 1 1 1 0.000000 10.0000 0
62 1 1 1 0.000000 10.0000 0
63 1 1 1 0.000000 10.0000 0
64 1 1 1 0.000000 10.0000 0
65 1 1 1 0.000000 10.0000 0
66 1 1 1 0.000000 10.0000 0
67 1 1 1 0.000000 10.0000 0
68 1 1 1 0.000000 10.0000 0
69 1 1 1 0.000000 10.0000 0
70 1 1 1 0.000000 10.0000 0
71 1 1 1 0.000000 10.0000 0
72 1 1 1 0.000000 10.0000 0
73 2 9 9 -0.180000 10.0000 0
74 2 4 4 0.090000 10.0000 0
75 2 4 4 0.090000 10.0000 0
76 2 9 9 -0.090000 10.0000 0
77 2 4 4 0.090000 10.0000 0
78 2 10 10 -0.180000 10.0000 0
79 2 5 5 0.090000 10.0000 0
80 2 5 5 0.090000 10.0000 0
81 2 11 11 -0.090000 10.0000 0
82 2 4 4 0.090000 10.0000 0
83 2 10 10 -0.180000 10.0000 0
84 2 5 5 0.090000 10.0000 0
85 2 5 5 0.090000 10.0000 0
86 2 12 12 -0.090000 10.0000 0
87 2 4 4 0.090000 10.0000 0
88 2 8 8 0.280000 10.0000 0
89 2 16 16 -0.710000 10.0000 0
90 2 7 7 0.340000 10.0000 0
91 2 3 3 0.120000 10.0000 0
92 2 14 14 -0.050000 10.0000 0
93 2 15 15 -0.740000 10.0000 0
94 2 7 7 0.500000 10.0000 0
95 2 3 3 0.130000 10.0000 0
96 2 15 15 -0.750000 10.0000 0
97 2 8 8 0.430000 10.0000 0
98 2 6 6 0.460000 10.0000 0
99 2 13 13 -0.770000 10.0000 0
100 2 2 2 0.380000 10.0000 0
101 2 2 2 0.380000 10.0000 0
102 3 9 9 -0.180000 10.0000 0
103 3 4 4 0.090000 10.0000 0
104 3 4 4 0.090000 10.0000 0
105 3 9 9 -0.090000 10.0000 0
106 3 4 4 0.090000 10.0000 0
107 3 10 10 -0.180000 10.0000 0
108 3 5 5 0.090000 10.0000 0
109 3 5 5 0.090000 10.0000 0
110 3 11 11 -0.090000 10.0000 0
111 3 4 4 0.090000 10.0000 0
112 3 10 10 -0.180000 10.0000 0
113 3 5 5 0.090000 10.0000 0
114 3 5 5 0.090000 10.0000 0
115 3 12 12 -0.090000 10.0000 0
116 3 4 4 0.090000 10.0000 0
117 3 8 8 0.280000 10.0000 0
118 3 16 16 -0.710000 10.0000 0
119 3 7 7 0.340000 10.0000 0
120 3 3 3 0.120000 10.0000 0
121 3 14 14 -0.050000 10.0000 0
122 3 15 15 -0.740000 10.0000 0
123 3 7 7 0.500000 10.0000 0
124 3 3 3 0.130000 10.0000 0
125 3 15 15 -0.750000 10.0000 0
126 3 8 8 0.430000 10.0000 0
127 3 6 6 0.460000 10.0000 0
128 3 13 13 -0.770000 10.0000 0
129 3 2 2 0.380000 10.0000 0
130 3 2 2 0.380000 10.0000 0
166 !NBOND: bonds
1 2 1 22 2 3 2 5
3 24 3 4 4 7 4 29
5 6 6 7 6 9 7 8
8 33 8 11 9 10 10 13
10 11 11 12 12 15 12 37
13 14 14 17 14 15 15 16
16 19 16 41 17 18 18 21
18 19 19 20 20 23 20 45
21 22 22 23 23 24 24 25
25 26 25 46 26 27 26 29
27 48 27 28 28 31 28 53
29 30 30 31 30 33 31 32
32 57 32 35 33 34 34 37
34 35 35 36 36 39 36 61
37 38 38 41 38 39 39 40
40 43 40 65 41 42 42 45
42 43 43 44 44 47 44 69
45 46 46 47 47 48 48 49
49 50 49 70 50 51 50 53
51 72 51 52 52 55 53 54
54 55 54 57 55 56 56 59
57 58 58 61 58 59 59 60
60 63 61 62 62 65 62 63
63 64 64 67 65 66 66 69
66 67 67 68 68 71 69 70
70 71 71 72 73 81 73 74
73 75 73 78 76 78 76 77
76 92 76 86 78 79 78 80
81 86 81 83 81 82 83 86
83 84 83 85 86 87 88 89
88 97 88 98 89 90 90 91
90 92 92 97 93 98 93 94
94 95 94 96 96 97 98 99
99 100 99 101 102 110 102 103
102 104 102 107 105 107 105 106
105 121 105 115 107 108 107 109
110 115 110 112 110 111 112 115
112 113 112 114 115 116 117 118
117 126 117 127 118 119 119 120
119 121 121 126 122 127 122 123
123 124 123 125 125 126 127 128
128 129 128 130
312 !NTHETA: angles
2 1 22 1 2 3 1 2 5
3 2 5 2 3 24 2 3 4
4 3 24 3 4 7 3 4 29
7 4 29 2 5 6 5 6 7
5 6 9 7 6 9 4 7 6
4 7 8 6 7 8 7 8 33
7 8 11 11 8 33 6 9 10
9 10 13 9 10 11 11 10 13
8 11 10 8 11 12 10 11 12
11 12 15 11 12 37 15 12 37
10 13 14 13 14 17 13 14 15
15 14 17 12 15 14 12 15 16
14 15 16 15 16 19 15 16 41
19 16 41 14 17 18 17 18 21
17 18 19 19 18 21 16 19 18
16 19 20 18 19 20 19 20 23
19 20 45 23 20 45 18 21 22
1 22 21 1 22 23 21 22 23
20 23 22 20 23 24 22 23 24
3 24 23 3 24 25 23 24 25
24 25 26 24 25 46 26 25 46
25 26 27 25 26 29 27 26 29
26 27 48 26 27 28 28 27 48
27 28 31 27 28 53 31 28 53
4 29 26 4 29 30 26 29 30
29 30 31 29 30 33 31 30 33
28 31 30 28 31 32 30 31 32
31 32 57 31 32 35 35 32 57
8 33 30 8 33 34 30 33 34
33 34 37 33 34 35 35 34 37
32 35 34 32 35 36 34 35 36
35 36 39 35 36 61 39 36 61
12 37 34 12 37 38 34 37 38
37 38 41 37 38 39 39 38 41
36 39 38 36 39 40 38 39 40
39 40 43 39 40 65 43 40 65
16 41 38 16 41 42 38 41 42
41 42 45 41 42 43 43 42 45
40 43 42 40 43 44 42 43 44
43 44 47 43 44 69 47 44 69
20 45 42 20 45 46 42 45 46
25 46 45 25 46 47 45 46 47
44 47 46 44 47 48 46 47 48
27 48 47 27 48 49 47 48 49
48 49 50 48 49 70 50 49 70
49 50 51 49 50 53 51 50 53
50 51 72 50 51 52 52 51 72
51 52 55 28 53 50 28 53 54
50 53 54 53 54 55 53 54 57
55 54 57 52 55 54 52 55 56
54 55 56 55 56 59 32 57 54
32 57 58 54 57 58 57 58 61
57 58 59 59 58 61 56 59 58
56 59 60 58 59 60 59 60 63
36 61 58 36 61 62 58 61 62
61 62 65 61 62 63 63 62 65
60 63 62 60 63 64 62 63 64
63 64 67 40 65 62 40 65 66
62 65 66 65 66 69 65 66 67
67 66 69 64 67 66 64 67 68
66 67 68 67 68 71 44 69 66
44 69 70 66 69 70 49 70 69
49 70 71 69 70 71 68 71 70
68 71 72 70 71 72 51 72 71
73 81 82 73 81 83 73 81 86
73 78 80 73 78 79 74 73 75
76 92 90 76 92 97 76 86 87
76 86 83 76 86 81 76 78 80
76 78 79 73 78 76 77 76 92
78 76 92 77 76 78 75 73 78
74 73 78 78 73 81 79 78 80
81 86 87 81 86 83 81 83 85
81 83 84 81 83 86 75 73 81
74 73 81 83 86 87 82 81 83
84 83 85 85 83 86 84 83 86
82 81 86 83 81 86 86 76 92
77 76 86 78 76 86 88 98 93
88 89 90 89 88 97 89 90 91
88 97 92 92 97 96 89 90 92
91 90 92 93 94 96 93 94 95
94 93 98 95 94 96 88 97 96
94 96 97 90 92 97 98 99 101
98 99 100 97 88 98 89 88 98
93 98 99 88 98 99 100 99 101
102 110 111 102 110 112 102 110 115
102 107 109 102 107 108 103 102 104
105 121 119 105 121 126 105 115 116
105 115 112 105 115 110 105 107 109
105 107 108 102 107 105 106 105 121
107 105 121 106 105 107 104 102 107
103 102 107 107 102 110 108 107 109
110 115 116 110 115 112 110 112 114
110 112 113 110 112 115 104 102 110
103 102 110 112 115 116 111 110 112
113 112 114 114 112 115 113 112 115
111 110 115 112 110 115 115 105 121
106 105 115 107 105 115 117 127 122
117 118 119 118 117 126 118 119 120
117 126 121 121 126 125 118 119 121
120 119 121 122 123 125 122 123 124
123 122 127 124 123 125 117 126 125
123 125 126 119 121 126 127 128 130
127 128 129 126 117 127 118 117 127
122 127 128 117 127 128 129 128 130
554 !NPHI: dihedrals
22 1 2 3 22 1 2 5
2 1 22 21 2 1 22 23
1 2 3 24 1 2 3 4
5 2 3 24 5 2 3 4
1 2 5 6 3 2 5 6
2 3 24 23 2 3 24 25
4 3 24 23 4 3 24 25
2 3 4 7 2 3 4 29
24 3 4 7 24 3 4 29
3 4 7 6 3 4 7 8
29 4 7 6 29 4 7 8
3 4 29 26 3 4 29 30
7 4 29 26 7 4 29 30
2 5 6 7 2 5 6 9
5 6 7 4 5 6 7 8
9 6 7 4 9 6 7 8
5 6 9 10 7 6 9 10
4 7 8 33 4 7 8 11
6 7 8 33 6 7 8 11
7 8 33 30 7 8 33 34
11 8 33 30 11 8 33 34
7 8 11 10 7 8 11 12
33 8 11 10 33 8 11 12
6 9 10 13 6 9 10 11
9 10 13 14 11 10 13 14
9 10 11 8 9 10 11 12
13 10 11 8 13 10 11 12
8 11 12 15 8 11 12 37
10 11 12 15 10 11 12 37
11 12 15 14 11 12 15 16
37 12 15 14 37 12 15 16
11 12 37 34 11 12 37 38
15 12 37 34 15 12 37 38
10 13 14 17 10 13 14 15
13 14 17 18 15 14 17 18
13 14 15 12 13 14 15 16
17 14 15 12 17 14 15 16
12 15 16 19 12 15 16 41
14 15 16 19 14 15 16 41
15 16 19 18 15 16 19 20
41 16 19 18 41 16 19 20
15 16 41 38 15 16 41 42
19 16 41 38 19 16 41 42
14 17 18 21 14 17 18 19
17 18 21 22 19 18 21 22
17 18 19 16 17 18 19 20
21 18 19 16 21 18 19 20
16 19 20 23 16 19 20 45
18 19 20 23 18 19 20 45
19 20 23 22 19 20 23 24
45 20 23 22 45 20 23 24
19 20 45 42 19 20 45 46
23 20 45 42 23 20 45 46
18 21 22 1 18 21 22 23
1 22 23 20 1 22 23 24
21 22 23 20 21 22 23 24
20 23 24 3 20 23 24 25
22 23 24 3 22 23 24 25
3 24 25 26 3 24 25 46
23 24 25 26 23 24 25 46
24 25 26 27 24 25 26 29
46 25 26 27 46 25 26 29
24 25 46 45 24 25 46 47
26 25 46 45 26 25 46 47
25 26 27 48 25 26 27 28
29 26 27 48 29 26 27 28
25 26 29 4 25 26 29 30
27 26 29 4 27 26 29 30
26 27 48 47 26 27 48 49
28 27 48 47 28 27 48 49
26 27 28 31 26 27 28 53
48 27 28 31 48 27 28 53
27 28 31 30 27 28 31 32
53 28 31 30 53 28 31 32
27 28 53 50 27 28 53 54
31 28 53 50 31 28 53 54
4 29 30 31 4 29 30 33
26 29 30 31 26 29 30 33
29 30 31 28 29 30 31 32
33 30 31 28 33 30 31 32
29 30 33 8 29 30 33 34
31 30 33 8 31 30 33 34
28 31 32 57 28 31 32 35
30 31 32 57 30 31 32 35
31 32 57 54 31 32 57 58
35 32 57 54 35 32 57 58
31 32 35 34 31 32 35 36
57 32 35 34 57 32 35 36
8 33 34 37 8 33 34 35
30 33 34 37 30 33 34 35
33 34 37 12 33 34 37 38
35 34 37 12 35 34 37 38
33 34 35 32 33 34 35 36
37 34 35 32 37 34 35 36
32 35 36 39 32 35 36 61
34 35 36 39 34 35 36 61
35 36 39 38 35 36 39 40
61 36 39 38 61 36 39 40
35 36 61 58 35 36 61 62
39 36 61 58 39 36 61 62
12 37 38 41 12 37 38 39
34 37 38 41 34 37 38 39
37 38 41 16 37 38 41 42
39 38 41 16 39 38 41 42
37 38 39 36 37 38 39 40
41 38 39 36 41 38 39 40
36 39 40 43 36 39 40 65
38 39 40 43 38 39 40 65
39 40 43 42 39 40 43 44
65 40 43 42 65 40 43 44
39 40 65 62 39 40 65 66
43 40 65 62 43 40 65 66
16 41 42 45 16 41 42 43
38 41 42 45 38 41 42 43
41 42 45 20 41 42 45 46
43 42 45 20 43 42 45 46
41 42 43 40 41 42 43 44
45 42 43 40 45 42 43 44
40 43 44 47 40 43 44 69
42 43 44 47 42 43 44 69
43 44 47 46 43 44 47 48
69 44 47 46 69 44 47 48
43 44 69 66 43 44 69 70
47 44 69 66 47 44 69 70
20 45 46 25 20 45 46 47
42 45 46 25 42 45 46 47
25 46 47 44 25 46 47 48
45 46 47 44 45 46 47 48
44 47 48 27 44 47 48 49
46 47 48 27 46 47 48 49
27 48 49 50 27 48 49 70
47 48 49 50 47 48 49 70
48 49 50 51 48 49 50 53
70 49 50 51 70 49 50 53
48 49 70 69 48 49 70 71
50 49 70 69 50 49 70 71
49 50 51 72 49 50 51 52
53 50 51 72 53 50 51 52
49 50 53 28 49 50 53 54
51 50 53 28 51 50 53 54
50 51 72 71 52 51 72 71
50 51 52 55 72 51 52 55
51 52 55 54 51 52 55 56
28 53 54 55 28 53 54 57
50 53 54 55 50 53 54 57
53 54 55 52 53 54 55 56
57 54 55 52 57 54 55 56
53 54 57 32 53 54 57 58
55 54 57 32 55 54 57 58
52 55 56 59 54 55 56 59
55 56 59 58 55 56 59 60
32 57 58 61 32 57 58 59
54 57 58 61 54 57 58 59
57 58 61 36 57 58 61 62
59 58 61 36 59 58 61 62
57 58 59 56 57 58 59 60
61 58 59 56 61 58 59 60
56 59 60 63 58 59 60 63
59 60 63 62 59 60 63 64
36 61 62 65 36 61 62 63
58 61 62 65 58 61 62 63
61 62 65 40 61 62 65 66
63 62 65 40 63 62 65 66
61 62 63 60 61 62 63 64
65 62 63 60 65 62 63 64
60 63 64 67 62 63 64 67
63 64 67 66 63 64 67 68
40 65 66 69 40 65 66 67
62 65 66 69 62 65 66 67
65 66 69 44 65 66 69 70
67 66 69 44 67 66 69 70
65 66 67 64 65 66 67 68
69 66 67 64 69 66 67 68
64 67 68 71 66 67 68 71
67 68 71 70 67 68 71 72
44 69 70 49 44 69 70 71
66 69 70 49 66 69 70 71
49 70 71 68 49 70 71 72
69 70 71 68 69 70 71 72
68 71 72 51 70 71 72 51
73 81 86 76 73 81 86 83
73 81 86 87 73 81 83 86
73 81 83 84 73 81 83 85
86 76 78 73 77 76 78 73
92 76 78 73 74 73 78 76
74 73 78 79 74 73 78 80
74 73 81 86 74 73 81 83
74 73 81 82 75 73 78 76
75 73 78 79 75 73 78 80
75 73 81 86 75 73 81 83
75 73 81 82 76 92 97 96
76 92 97 88 91 90 92 76
89 90 92 76 83 81 86 76
82 81 86 76 81 83 86 76
84 83 86 76 85 83 86 76
81 73 78 76 77 76 86 81
77 76 86 83 77 76 86 87
77 76 78 79 77 76 78 80
77 76 92 97 77 76 92 90
78 76 86 81 78 76 86 83
78 76 86 87 78 76 92 97
78 76 92 90 78 73 81 86
78 73 81 83 78 73 81 82
86 76 78 79 92 76 78 79
81 73 78 79 86 76 78 80
92 76 78 80 81 73 78 80
92 76 86 81 84 83 86 81
85 83 86 81 81 83 86 87
82 81 86 83 82 81 86 87
82 81 83 86 82 81 83 84
82 81 83 85 92 76 86 83
83 81 86 87 86 81 83 84
84 83 86 87 86 81 83 85
85 83 86 87 86 76 92 97
86 76 92 90 92 76 86 87
88 98 99 100 88 98 99 101
94 93 98 88 90 92 97 88
94 96 97 88 88 89 90 92
88 89 90 91 89 90 92 97
89 88 98 99 89 88 98 93
89 88 97 92 89 88 97 96
90 92 97 96 98 88 89 90
97 88 89 90 91 90 92 97
94 96 97 92 98 88 97 92
93 98 99 100 93 98 99 101
97 88 98 93 93 94 96 97
94 93 98 99 98 93 94 95
95 94 96 97 98 88 97 96
98 93 94 96 102 110 115 105
102 110 115 112 102 110 115 116
102 110 112 115 102 110 112 113
102 110 112 114 115 105 107 102
106 105 107 102 121 105 107 102
103 102 107 105 103 102 107 108
103 102 107 109 103 102 110 115
103 102 110 112 103 102 110 111
104 102 107 105 104 102 107 108
104 102 107 109 104 102 110 115
104 102 110 112 104 102 110 111
105 121 126 125 105 121 126 117
120 119 121 105 118 119 121 105
112 110 115 105 111 110 115 105
110 112 115 105 113 112 115 105
114 112 115 105 110 102 107 105
106 105 115 110 106 105 115 112
106 105 115 116 106 105 107 108
106 105 107 109 106 105 121 126
106 105 121 119 107 105 115 110
107 105 115 112 107 105 115 116
107 105 121 126 107 105 121 119
107 102 110 115 107 102 110 112
107 102 110 111 115 105 107 108
121 105 107 108 110 102 107 108
115 105 107 109 121 105 107 109
110 102 107 109 121 105 115 110
113 112 115 110 114 112 115 110
110 112 115 116 111 110 115 112
111 110 115 116 111 110 112 115
111 110 112 113 111 110 112 114
121 105 115 112 112 110 115 116
115 110 112 113 113 112 115 116
115 110 112 114 114 112 115 116
115 105 121 126 115 105 121 119
121 105 115 116 117 127 128 129
117 127 128 130 123 122 127 117
119 121 126 117 123 125 126 117
117 118 119 121 117 118 119 120
118 119 121 126 118 117 127 128
118 117 127 122 118 117 126 121
118 117 126 125 119 121 126 125
127 117 118 119 126 117 118 119
120 119 121 126 123 125 126 121
127 117 126 121 122 127 128 129
122 127 128 130 126 117 127 122
122 123 125 126 123 122 127 128
127 122 123 124 124 123 125 126
127 117 126 125 127 122 123 125
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0
1 0 !NGRP
0 0 0

489
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf Normal file
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PSF
1 !NTITLE
REMARKS VMD generated structure x-plor psf file
101 !NATOM
1 2 1 1 0.000000 10.0000 0
2 2 1 1 0.000000 10.0000 0
3 2 1 1 0.000000 10.0000 0
4 2 1 1 0.000000 10.0000 0
5 2 1 1 0.000000 10.0000 0
6 2 1 1 0.000000 10.0000 0
7 2 1 1 0.000000 10.0000 0
8 2 1 1 0.000000 10.0000 0
9 2 1 1 0.000000 10.0000 0
10 2 1 1 0.000000 10.0000 0
11 2 1 1 0.000000 10.0000 0
12 2 1 1 0.000000 10.0000 0
13 2 1 1 0.000000 10.0000 0
14 2 1 1 0.000000 10.0000 0
15 2 1 1 0.000000 10.0000 0
16 2 1 1 0.000000 10.0000 0
17 2 1 1 0.000000 10.0000 0
18 2 1 1 0.000000 10.0000 0
19 2 1 1 0.000000 10.0000 0
20 2 1 1 0.000000 10.0000 0
21 2 1 1 0.000000 10.0000 0
22 2 1 1 0.000000 10.0000 0
23 2 1 1 0.000000 10.0000 0
24 2 1 1 0.000000 10.0000 0
25 2 1 1 0.000000 10.0000 0
26 2 1 1 0.000000 10.0000 0
27 2 1 1 0.000000 10.0000 0
28 2 1 1 0.000000 10.0000 0
29 2 1 1 0.000000 10.0000 0
30 2 1 1 0.000000 10.0000 0
31 2 1 1 0.000000 10.0000 0
32 2 1 1 0.000000 10.0000 0
33 2 1 1 0.000000 10.0000 0
34 2 1 1 0.000000 10.0000 0
35 2 1 1 0.000000 10.0000 0
36 2 1 1 0.000000 10.0000 0
37 2 1 1 0.000000 10.0000 0
38 2 1 1 0.000000 10.0000 0
39 2 1 1 0.000000 10.0000 0
40 2 1 1 0.000000 10.0000 0
41 2 1 1 0.000000 10.0000 0
42 2 1 1 0.000000 10.0000 0
43 2 1 1 0.000000 10.0000 0
44 2 1 1 0.000000 10.0000 0
45 2 1 1 0.000000 10.0000 0
46 2 1 1 0.000000 10.0000 0
47 2 1 1 0.000000 10.0000 0
48 2 1 1 0.000000 10.0000 0
49 2 1 1 0.000000 10.0000 0
50 2 1 1 0.000000 10.0000 0
51 2 1 1 0.000000 10.0000 0
52 2 1 1 0.000000 10.0000 0
53 2 1 1 0.000000 10.0000 0
54 2 1 1 0.000000 10.0000 0
55 2 1 1 0.000000 10.0000 0
56 2 1 1 0.000000 10.0000 0
57 2 1 1 0.000000 10.0000 0
58 2 1 1 0.000000 10.0000 0
59 2 1 1 0.000000 10.0000 0
60 2 1 1 0.000000 10.0000 0
61 2 1 1 0.000000 10.0000 0
62 2 1 1 0.000000 10.0000 0
63 2 1 1 0.000000 10.0000 0
64 2 1 1 0.000000 10.0000 0
65 2 1 1 0.000000 10.0000 0
66 2 1 1 0.000000 10.0000 0
67 2 1 1 0.000000 10.0000 0
68 2 1 1 0.000000 10.0000 0
69 2 1 1 0.000000 10.0000 0
70 2 1 1 0.000000 10.0000 0
71 2 1 1 0.000000 10.0000 0
72 2 1 1 0.000000 10.0000 0
73 1 9 9 -0.180000 10.0000 0
74 1 4 4 0.090000 10.0000 0
75 1 4 4 0.090000 10.0000 0
76 1 9 9 -0.090000 10.0000 0
77 1 4 4 0.090000 10.0000 0
78 1 10 10 -0.180000 10.0000 0
79 1 5 5 0.090000 10.0000 0
80 1 5 5 0.090000 10.0000 0
81 1 11 11 -0.090000 10.0000 0
82 1 4 4 0.090000 10.0000 0
83 1 10 10 -0.180000 10.0000 0
84 1 5 5 0.090000 10.0000 0
85 1 5 5 0.090000 10.0000 0
86 1 12 12 -0.090000 10.0000 0
87 1 4 4 0.090000 10.0000 0
88 1 8 8 0.280000 10.0000 0
89 1 16 16 -0.710000 10.0000 0
90 1 7 7 0.340000 10.0000 0
91 1 3 3 0.120000 10.0000 0
92 1 14 14 -0.050000 10.0000 0
93 1 15 15 -0.740000 10.0000 0
94 1 7 7 0.500000 10.0000 0
95 1 3 3 0.130000 10.0000 0
96 1 15 15 -0.750000 10.0000 0
97 1 8 8 0.430000 10.0000 0
98 1 6 6 0.460000 10.0000 0
99 1 13 13 -0.770000 10.0000 0
100 1 2 2 0.380000 10.0000 0
101 1 2 2 0.380000 10.0000 0
134 !NBOND: bonds
1 2 1 22 2 3 2 5
3 24 3 4 4 7 4 29
5 6 6 7 6 9 7 8
8 33 8 11 9 10 10 13
10 11 11 12 12 15 12 37
13 14 14 17 14 15 15 16
16 19 16 41 17 18 18 21
18 19 19 20 20 23 20 45
21 22 22 23 23 24 24 25
25 26 25 46 26 27 26 29
27 48 27 28 28 31 28 53
29 30 30 31 30 33 31 32
32 57 32 35 33 34 34 37
34 35 35 36 36 39 36 61
37 38 38 41 38 39 39 40
40 43 40 65 41 42 42 45
42 43 43 44 44 47 44 69
45 46 46 47 47 48 48 49
49 50 49 70 50 51 50 53
51 72 51 52 52 55 53 54
54 55 54 57 55 56 56 59
57 58 58 61 58 59 59 60
60 63 61 62 62 65 62 63
63 64 64 67 65 66 66 69
66 67 67 68 68 71 69 70
70 71 71 72 73 81 73 74
73 75 73 78 76 78 76 77
76 92 76 86 78 79 78 80
81 86 81 83 81 82 83 86
83 84 83 85 86 87 88 89
88 97 88 98 89 90 90 91
90 92 92 97 93 98 93 94
94 95 94 96 96 97 98 99
99 100 99 101
252 !NTHETA: angles
2 1 22 1 2 3 1 2 5
3 2 5 2 3 24 2 3 4
4 3 24 3 4 7 3 4 29
7 4 29 2 5 6 5 6 7
5 6 9 7 6 9 4 7 6
4 7 8 6 7 8 7 8 33
7 8 11 11 8 33 6 9 10
9 10 13 9 10 11 11 10 13
8 11 10 8 11 12 10 11 12
11 12 15 11 12 37 15 12 37
10 13 14 13 14 17 13 14 15
15 14 17 12 15 14 12 15 16
14 15 16 15 16 19 15 16 41
19 16 41 14 17 18 17 18 21
17 18 19 19 18 21 16 19 18
16 19 20 18 19 20 19 20 23
19 20 45 23 20 45 18 21 22
1 22 21 1 22 23 21 22 23
20 23 22 20 23 24 22 23 24
3 24 23 3 24 25 23 24 25
24 25 26 24 25 46 26 25 46
25 26 27 25 26 29 27 26 29
26 27 48 26 27 28 28 27 48
27 28 31 27 28 53 31 28 53
4 29 26 4 29 30 26 29 30
29 30 31 29 30 33 31 30 33
28 31 30 28 31 32 30 31 32
31 32 57 31 32 35 35 32 57
8 33 30 8 33 34 30 33 34
33 34 37 33 34 35 35 34 37
32 35 34 32 35 36 34 35 36
35 36 39 35 36 61 39 36 61
12 37 34 12 37 38 34 37 38
37 38 41 37 38 39 39 38 41
36 39 38 36 39 40 38 39 40
39 40 43 39 40 65 43 40 65
16 41 38 16 41 42 38 41 42
41 42 45 41 42 43 43 42 45
40 43 42 40 43 44 42 43 44
43 44 47 43 44 69 47 44 69
20 45 42 20 45 46 42 45 46
25 46 45 25 46 47 45 46 47
44 47 46 44 47 48 46 47 48
27 48 47 27 48 49 47 48 49
48 49 50 48 49 70 50 49 70
49 50 51 49 50 53 51 50 53
50 51 72 50 51 52 52 51 72
51 52 55 28 53 50 28 53 54
50 53 54 53 54 55 53 54 57
55 54 57 52 55 54 52 55 56
54 55 56 55 56 59 32 57 54
32 57 58 54 57 58 57 58 61
57 58 59 59 58 61 56 59 58
56 59 60 58 59 60 59 60 63
36 61 58 36 61 62 58 61 62
61 62 65 61 62 63 63 62 65
60 63 62 60 63 64 62 63 64
63 64 67 40 65 62 40 65 66
62 65 66 65 66 69 65 66 67
67 66 69 64 67 66 64 67 68
66 67 68 67 68 71 44 69 66
44 69 70 66 69 70 49 70 69
49 70 71 69 70 71 68 71 70
68 71 72 70 71 72 51 72 71
73 81 82 73 81 83 73 81 86
73 78 80 73 78 79 74 73 75
76 92 90 76 92 97 76 86 87
76 86 83 76 86 81 76 78 80
76 78 79 73 78 76 77 76 92
78 76 92 77 76 78 75 73 78
74 73 78 78 73 81 79 78 80
81 86 87 81 86 83 81 83 85
81 83 84 81 83 86 75 73 81
74 73 81 83 86 87 82 81 83
84 83 85 85 83 86 84 83 86
82 81 86 83 81 86 86 76 92
77 76 86 78 76 86 88 98 93
88 89 90 89 88 97 89 90 91
88 97 92 92 97 96 89 90 92
91 90 92 93 94 96 93 94 95
94 93 98 95 94 96 88 97 96
94 96 97 90 92 97 98 99 101
98 99 100 97 88 98 89 88 98
93 98 99 88 98 99 100 99 101
457 !NPHI: dihedrals
22 1 2 3 22 1 2 5
2 1 22 21 2 1 22 23
1 2 3 24 1 2 3 4
5 2 3 24 5 2 3 4
1 2 5 6 3 2 5 6
2 3 24 23 2 3 24 25
4 3 24 23 4 3 24 25
2 3 4 7 2 3 4 29
24 3 4 7 24 3 4 29
3 4 7 6 3 4 7 8
29 4 7 6 29 4 7 8
3 4 29 26 3 4 29 30
7 4 29 26 7 4 29 30
2 5 6 7 2 5 6 9
5 6 7 4 5 6 7 8
9 6 7 4 9 6 7 8
5 6 9 10 7 6 9 10
4 7 8 33 4 7 8 11
6 7 8 33 6 7 8 11
7 8 33 30 7 8 33 34
11 8 33 30 11 8 33 34
7 8 11 10 7 8 11 12
33 8 11 10 33 8 11 12
6 9 10 13 6 9 10 11
9 10 13 14 11 10 13 14
9 10 11 8 9 10 11 12
13 10 11 8 13 10 11 12
8 11 12 15 8 11 12 37
10 11 12 15 10 11 12 37
11 12 15 14 11 12 15 16
37 12 15 14 37 12 15 16
11 12 37 34 11 12 37 38
15 12 37 34 15 12 37 38
10 13 14 17 10 13 14 15
13 14 17 18 15 14 17 18
13 14 15 12 13 14 15 16
17 14 15 12 17 14 15 16
12 15 16 19 12 15 16 41
14 15 16 19 14 15 16 41
15 16 19 18 15 16 19 20
41 16 19 18 41 16 19 20
15 16 41 38 15 16 41 42
19 16 41 38 19 16 41 42
14 17 18 21 14 17 18 19
17 18 21 22 19 18 21 22
17 18 19 16 17 18 19 20
21 18 19 16 21 18 19 20
16 19 20 23 16 19 20 45
18 19 20 23 18 19 20 45
19 20 23 22 19 20 23 24
45 20 23 22 45 20 23 24
19 20 45 42 19 20 45 46
23 20 45 42 23 20 45 46
18 21 22 1 18 21 22 23
1 22 23 20 1 22 23 24
21 22 23 20 21 22 23 24
20 23 24 3 20 23 24 25
22 23 24 3 22 23 24 25
3 24 25 26 3 24 25 46
23 24 25 26 23 24 25 46
24 25 26 27 24 25 26 29
46 25 26 27 46 25 26 29
24 25 46 45 24 25 46 47
26 25 46 45 26 25 46 47
25 26 27 48 25 26 27 28
29 26 27 48 29 26 27 28
25 26 29 4 25 26 29 30
27 26 29 4 27 26 29 30
26 27 48 47 26 27 48 49
28 27 48 47 28 27 48 49
26 27 28 31 26 27 28 53
48 27 28 31 48 27 28 53
27 28 31 30 27 28 31 32
53 28 31 30 53 28 31 32
27 28 53 50 27 28 53 54
31 28 53 50 31 28 53 54
4 29 30 31 4 29 30 33
26 29 30 31 26 29 30 33
29 30 31 28 29 30 31 32
33 30 31 28 33 30 31 32
29 30 33 8 29 30 33 34
31 30 33 8 31 30 33 34
28 31 32 57 28 31 32 35
30 31 32 57 30 31 32 35
31 32 57 54 31 32 57 58
35 32 57 54 35 32 57 58
31 32 35 34 31 32 35 36
57 32 35 34 57 32 35 36
8 33 34 37 8 33 34 35
30 33 34 37 30 33 34 35
33 34 37 12 33 34 37 38
35 34 37 12 35 34 37 38
33 34 35 32 33 34 35 36
37 34 35 32 37 34 35 36
32 35 36 39 32 35 36 61
34 35 36 39 34 35 36 61
35 36 39 38 35 36 39 40
61 36 39 38 61 36 39 40
35 36 61 58 35 36 61 62
39 36 61 58 39 36 61 62
12 37 38 41 12 37 38 39
34 37 38 41 34 37 38 39
37 38 41 16 37 38 41 42
39 38 41 16 39 38 41 42
37 38 39 36 37 38 39 40
41 38 39 36 41 38 39 40
36 39 40 43 36 39 40 65
38 39 40 43 38 39 40 65
39 40 43 42 39 40 43 44
65 40 43 42 65 40 43 44
39 40 65 62 39 40 65 66
43 40 65 62 43 40 65 66
16 41 42 45 16 41 42 43
38 41 42 45 38 41 42 43
41 42 45 20 41 42 45 46
43 42 45 20 43 42 45 46
41 42 43 40 41 42 43 44
45 42 43 40 45 42 43 44
40 43 44 47 40 43 44 69
42 43 44 47 42 43 44 69
43 44 47 46 43 44 47 48
69 44 47 46 69 44 47 48
43 44 69 66 43 44 69 70
47 44 69 66 47 44 69 70
20 45 46 25 20 45 46 47
42 45 46 25 42 45 46 47
25 46 47 44 25 46 47 48
45 46 47 44 45 46 47 48
44 47 48 27 44 47 48 49
46 47 48 27 46 47 48 49
27 48 49 50 27 48 49 70
47 48 49 50 47 48 49 70
48 49 50 51 48 49 50 53
70 49 50 51 70 49 50 53
48 49 70 69 48 49 70 71
50 49 70 69 50 49 70 71
49 50 51 72 49 50 51 52
53 50 51 72 53 50 51 52
49 50 53 28 49 50 53 54
51 50 53 28 51 50 53 54
50 51 72 71 52 51 72 71
50 51 52 55 72 51 52 55
51 52 55 54 51 52 55 56
28 53 54 55 28 53 54 57
50 53 54 55 50 53 54 57
53 54 55 52 53 54 55 56
57 54 55 52 57 54 55 56
53 54 57 32 53 54 57 58
55 54 57 32 55 54 57 58
52 55 56 59 54 55 56 59
55 56 59 58 55 56 59 60
32 57 58 61 32 57 58 59
54 57 58 61 54 57 58 59
57 58 61 36 57 58 61 62
59 58 61 36 59 58 61 62
57 58 59 56 57 58 59 60
61 58 59 56 61 58 59 60
56 59 60 63 58 59 60 63
59 60 63 62 59 60 63 64
36 61 62 65 36 61 62 63
58 61 62 65 58 61 62 63
61 62 65 40 61 62 65 66
63 62 65 40 63 62 65 66
61 62 63 60 61 62 63 64
65 62 63 60 65 62 63 64
60 63 64 67 62 63 64 67
63 64 67 66 63 64 67 68
40 65 66 69 40 65 66 67
62 65 66 69 62 65 66 67
65 66 69 44 65 66 69 70
67 66 69 44 67 66 69 70
65 66 67 64 65 66 67 68
69 66 67 64 69 66 67 68
64 67 68 71 66 67 68 71
67 68 71 70 67 68 71 72
44 69 70 49 44 69 70 71
66 69 70 49 66 69 70 71
49 70 71 68 49 70 71 72
69 70 71 68 69 70 71 72
68 71 72 51 70 71 72 51
73 81 86 76 73 81 86 83
73 81 86 87 73 81 83 86
73 81 83 84 73 81 83 85
86 76 78 73 77 76 78 73
92 76 78 73 74 73 78 76
74 73 78 79 74 73 78 80
74 73 81 86 74 73 81 83
74 73 81 82 75 73 78 76
75 73 78 79 75 73 78 80
75 73 81 86 75 73 81 83
75 73 81 82 76 92 97 96
76 92 97 88 91 90 92 76
89 90 92 76 83 81 86 76
82 81 86 76 81 83 86 76
84 83 86 76 85 83 86 76
81 73 78 76 77 76 86 81
77 76 86 83 77 76 86 87
77 76 78 79 77 76 78 80
77 76 92 97 77 76 92 90
78 76 86 81 78 76 86 83
78 76 86 87 78 76 92 97
78 76 92 90 78 73 81 86
78 73 81 83 78 73 81 82
86 76 78 79 92 76 78 79
81 73 78 79 86 76 78 80
92 76 78 80 81 73 78 80
92 76 86 81 84 83 86 81
85 83 86 81 81 83 86 87
82 81 86 83 82 81 86 87
82 81 83 86 82 81 83 84
82 81 83 85 92 76 86 83
83 81 86 87 86 81 83 84
84 83 86 87 86 81 83 85
85 83 86 87 86 76 92 97
86 76 92 90 92 76 86 87
88 98 99 100 88 98 99 101
94 93 98 88 90 92 97 88
94 96 97 88 88 89 90 92
88 89 90 91 89 90 92 97
89 88 98 99 89 88 98 93
89 88 97 92 89 88 97 96
90 92 97 96 98 88 89 90
97 88 89 90 91 90 92 97
94 96 97 92 98 88 97 92
93 98 99 100 93 98 99 101
97 88 98 93 93 94 96 97
94 93 98 99 98 93 94 95
95 94 96 97 98 88 97 96
98 93 94 96
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0
1 0 !NGRP
0 0 0

1
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in Normal file
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atom_style full

46
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt Normal file
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###########################################################
# Interaction of a carbon nanotube with a pair of mystery
# molecules (extracted from the cnat-cnt.data/in files).
###########################################################
#
# define the system being simulated:
# -- init section --
include system.in.init
# -- atom definition section --
read_data system.data
# -- settings section --
include system.in.settings
# -- run section --
timestep 0.05
dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz
# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking
# dynamics in dilute systems with few atoms (such as this one).
# Commenting this next line out:
# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
# Alternately, I receive fewer questions if I use langevin/nve instead:
fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5
fix fxnve all nve
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
thermo 500 # time interval for printing out "thermo" data
#thermo_modify flush yes
#restart 1000000 restart_nvt
run 500000
write_data system_after_nvt.data

29
tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt Normal file
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#Define the CNT and CNAD molecules, by including the files which define them
import cnt.lt
import cnad.lt
# The cnt's center was originally at position 10,10,10,
# so I moved it back to the origin
cnt = new CNT.move(-10,-10,-10)
# Rotation around the center of mass does not work (yet),
# so instead you have to move the molecule to the origin,
# rotate it, and move it back to where you want it.
# That's why the next line contains move().rot().move()
# I'll add center-of-mass rotation as a later feature.
cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0)
cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0)
# You can leave the periodic boundary conditions unspecified
# and change them later, OR you can declare them
# using the "write_once("Data Boundary") {}" command:
write_once("Data Boundary")
{
0 50.0 xlo xhi
0 50.0 ylo yhi
0 50.0 zlo zhi
}

10
tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT Normal file
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This is a simple system of 260 water molecules.
In this example, the coordinates of the atoms are read from a PDB file
instead of being specified manually (as well as the boundary information).
The PDB file was generated by the useful "solvate" utility which comes with VMD.
(To generate this file yourself, run VMD, click on the "Extensions" menu,
and select Modeling-->Add Solvation Box.
In this example, I made a box whose x,y,z dimensions were 16,24,24.)

31
tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh Executable file
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# --- Running LAMMPS ---
# -- Prerequisites: --
# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
# input scripts which link to the input scripts and data files
# you hopefully have created earlier with moltemplate.sh:
# system.in.init, system.in.settings, system.data
# If not, carry out the instructions in "README_setup.sh".
#
# -- Instructions: --
# If "lmp_linux" is the name of the command you use to invoke lammps,
# then you would run lammps on these files this way:
lmp_linux -i run.in.npt # minimization and simulation at constant pressure
lmp_linux -i run.in.nvt # minimization and simulation at constant volume
#(Note: The constant volume simulation lacks pressure equilibration. These are
# completely separate simulations. The results of the constant pressure
# simulation are ignored when beginning the simulation at constant volume.
# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
# If you have compiled the MPI version of lammps, you can run lammps in parallel
#mpirun -np 4 lmp_linux -i run.in.npt
#mpirun -np 4 lmp_linux -i run.in.nvt
# (assuming you have 4 processors available)

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# Use these commands to generate the LAMMPS input script and data file
# (and other auxilliary files):
cd moltemplate_files/ # (The .lt input files are in this directory)
moltemplate.sh -pdb solvate.pdb system.lt
# This will generate various files with names ending in *.in* and *.data.
# These files are the input files directly read by LAMMPS. Move them to
# the parent directory (or wherever you plan to run the simulation).
mv -f system.in* system.data ../
# Optional:
# The "./output_ttree/" directory is full of temporary files generated by
# moltemplate. They can be useful for debugging, but are usually thrown away.
rm -rf output_ttree/
cd ../
#
#This will prepare LAMMPS input files for a box of water
#(In this example, we are using the "SPC/E" water model.)
#The number of water molecules in the "wat = new SPCE [260]" command
#must equal the number of water molecules in the PDB file.
#
#Coordinates and boundary-box information is read from the .pdb file.
#
#You can also specify this information directly in the ttree file.
#See the comments section in "system.lt" for details.
#

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------- Instructions to view a trajectory in VMD --------
------- Disclaimer -------
1) Build a PSF file for use in viewing with VMD.
This step works with VMD 1.9 and topotools 1.2.
(Older versions, like VMD 1.8.6, don't support this.)
a) Start VMD
b) Menu Extensions->Tk Console
c) Enter:
(I assume that the the DATA file is called "system.data")
topo readlammpsdata system.data full
animate write psf system.psf
(Note, at this point the image shown in the VMD graphics window may
not appear correct or incomplete. The coordinates of the atoms may
overlap if you asked moltemplate.sh to load your coordinates from
a PDB or XYZ file.
However, later after you have run a simulation, the trajectories
should appear reasonably correct when you load them in VMD using
the PSF file you just generated.)
Later, to Load a trajectory in VMD:
Start VMD
Select menu: File->New Molecule
-Browse to select the PSF file you created above, and load it.
(Don't close the window yet.)
-Browse to select the trajectory file.
If necessary, for "file type" select: "LAMMPS Trajectory"
Load it
----- Wrap the coordinates to the unit cell
a) Start VMD
b) Load the trajectory in VMD (see above)
c) Menu Extensions->Tk Console
d) Enter:
DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT.
LOOKUP "pbctools" FOR DETAILS.
pbc wrap -compound res -all
pbc box
# If you have a solute of type 1, then use this:
#pbc wrap -sel type=1 -all -centersel type=2 -center com
"1" corresponds to the "O" atom type
"2" corresponds to the "H" atom type
3) Optional: If you like, change the atom types in the PSF file so
that VMD recognizes the atom types:
sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf
sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf
(If you do this, I guess that you might have to use
"type=O" and "type=H" in step 2 above.)

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# Run moltemplate this way:
moltemplate.sh -pdb solvate.pdb system.lt
# The PDB file was generated by the "solvate" utility which comes with VMD.
# (To generate this file yourself, run VMD, click on the "Extensions" menu,
# and select Modeling-->Add Solvation Box.
# In this example, I made a box whose x,y,z dimensions were 16,24,24.)

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CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1
ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O
ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H
ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H
ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O
ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H
ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H
ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O
ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H
ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H
ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O
ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H
ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H
ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O
ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H
ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H
ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O
ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H
ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H
ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O
ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H
ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H
ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O
ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H
ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H
ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O
ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H
ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H
ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O
ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H
ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H
ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O
ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H
ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H
ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O
ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H
ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H
ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O
ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H
ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H
ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O
ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H
ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H
ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O
ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H
ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H
ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O
ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H
ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H
ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O
ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H
ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H
ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O
ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H
ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H
ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O
ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H
ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H
ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O
ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H
ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H
ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O
ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H
ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H
ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O
ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H
ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H
ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O
ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H
ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H
ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O
ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H
ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H
ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O
ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H
ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H
ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O
ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H
ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H
ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O
ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H
ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H
ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O
ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H
ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H
ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O
ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H
ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H
ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O
ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H
ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H
ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O
ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H
ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H
ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O
ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H
ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H
ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O
ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H
ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H
ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O
ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H
ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H
ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O
ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H
ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H
ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O
ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H
ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H
ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O
ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H
ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H
ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O
ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H
ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H
ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O
ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H
ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H
ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O
ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H
ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H
ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O
ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H
ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H
ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O
ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H
ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H
ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O
ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H
ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H
ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O
ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H
ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H
ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O
ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H
ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H
ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O
ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H
ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H
ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O
ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H
ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H
ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O
ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H
ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H
ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O
ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H
ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H
ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O
ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H
ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H
ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O
ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H
ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H
ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O
ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H
ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H
ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O
ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H
ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H
ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O
ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H
ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H
ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O
ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H
ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H
ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O
ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H
ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H
ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O
ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H
ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H
ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O
ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H
ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H
ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O
ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H
ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H
ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O
ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H
ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H
ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O
ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H
ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H
ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O
ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H
ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H
ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O
ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H
ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H
ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O
ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H
ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H
ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O
ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H
ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H
ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O
ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H
ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H
ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O
ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H
ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H
ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O
ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H
ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H
ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O
ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H
ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H
ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O
ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H
ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H
ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O
ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H
ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H
ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O
ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H
ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H
ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O
ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H
ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H
ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O
ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H
ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H
ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O
ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H
ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H
ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O
ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H
ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H
ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O
ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H
ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H
ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O
ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H
ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H
ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O
ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H
ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H
ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O
ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H
ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H
ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O
ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H
ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H
ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O
ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H
ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H
ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O
ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H
ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H
ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O
ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H
ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H
ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O
ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H
ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H
ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O
ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H
ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H
ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O
ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H
ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H
ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O
ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H
ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H
ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O
ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H
ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H
ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O
ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H
ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H
ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O
ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H
ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H
ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O
ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H
ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H
ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O
ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H
ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H
ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O
ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H
ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H
ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O
ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H
ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H
ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O
ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H
ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H
ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O
ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H
ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H
ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O
ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H
ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H
ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O
ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H
ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H
ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O
ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H
ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H
ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O
ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H
ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H
ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O
ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H
ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H
ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O
ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H
ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H
ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O
ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H
ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H
ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O
ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H
ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H
ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O
ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H
ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H
ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O
ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H
ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H
ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O
ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H
ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H
ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O
ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H
ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H
ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O
ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H
ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H
ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O
ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H
ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H
ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O
ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H
ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H
ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O
ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H
ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H
ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O
ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H
ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H
ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O
ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H
ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H
ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O
ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H
ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H
ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O
ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H
ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H
ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O
ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H
ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H
ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O
ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H
ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H
ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O
ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H
ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H
ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O
ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H
ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H
ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O
ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H
ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H
ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O
ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H
ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H
ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O
ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H
ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H
ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O
ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H
ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H
ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O
ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H
ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H
ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O
ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H
ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H
ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O
ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H
ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H
ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O
ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H
ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H
ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O
ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H
ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H
ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O
ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H
ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H
ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O
ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H
ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H
ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O
ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H
ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H
ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O
ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H
ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H
ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O
ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H
ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H
ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O
ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H
ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H
ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O
ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H
ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H
ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O
ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H
ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H
ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O
ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H
ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H
ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O
ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H
ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H
ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O
ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H
ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H
ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O
ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H
ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H
ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O
ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H
ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H
ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O
ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H
ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H
ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O
ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H
ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H
ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O
ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H
ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H
ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O
ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H
ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H
ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O
ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H
ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H
ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O
ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H
ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H
ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O
ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H
ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H
ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O
ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H
ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H
ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O
ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H
ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H
ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O
ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H
ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H
ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O
ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H
ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H
ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O
ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H
ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H
ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O
ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H
ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H
ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O
ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H
ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H
ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O
ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H
ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H
ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O
ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H
ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H
ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O
ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H
ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H
ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O
ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H
ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H
ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O
ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H
ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H
ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O
ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H
ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H
ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O
ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H
ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H
ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O
ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H
ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H
ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O
ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H
ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H
ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O
ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H
ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H
ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O
ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H
ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H
ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O
ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H
ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H
ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O
ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H
ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H
ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O
ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H
ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H
ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O
ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H
ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H
ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O
ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H
ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H
ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O
ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H
ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H
ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O
ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H
ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H
ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O
ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H
ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H
ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O
ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H
ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H
ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O
ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H
ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H
ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O
ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H
ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H
ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O
ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H
ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H
ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O
ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H
ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H
ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O
ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H
ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H
ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O
ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H
ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H
ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O
ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H
ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H
ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O
ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H
ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H
ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O
ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H
ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H
ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O
ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H
ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H
ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O
ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H
ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H
ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O
ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H
ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H
ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O
ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H
ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H
ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O
ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H
ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H
ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O
ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H
ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H
ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O
ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H
ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H
ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O
ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H
ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H
ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O
ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H
ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H
ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O
ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H
ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H
ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O
ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H
ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H
ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O
ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H
ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H
ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O
ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H
ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H
ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O
ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H
ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H
ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O
ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H
ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H
ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O
ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H
ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H
ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O
ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H
ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H
ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O
ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H
ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H
ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O
ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H
ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H
ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O
ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H
ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H
ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O
ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H
ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H
ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O
ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H
ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H
ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O
ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H
ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H
ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O
ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H
ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H
ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O
ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H
ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H
ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O
ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H
ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H
ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O
ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H
ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H
ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O
ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H
ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H
ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O
ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H
ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H
ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O
ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H
ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H
ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O
ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H
ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H
ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O
ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H
ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H
ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O
ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H
ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H
ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O
ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H
ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H
ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O
ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H
ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H
ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O
ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H
ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H
ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O
ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H
ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H
ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O
ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H
ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H
ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O
ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H
ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H
ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O
ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H
ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H
ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O
ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H
ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H
ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O
ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H
ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H
ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O
ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H
ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H
ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O
ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H
ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H
ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O
ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H
ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H
ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O
ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H
ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H
ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O
ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H
ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H
ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O
ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H
ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H
ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O
ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H
ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H
ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O
ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H
ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H
ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O
ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H
ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H
ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O
ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H
ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H
ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O
ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H
ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H
ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O
ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H
ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H
ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O
ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H
ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H
ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O
ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H
ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H
ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O
ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H
ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H
ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O
ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H
ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H
ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O
ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H
ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H
ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O
ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H
ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H
ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O
ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H
ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H
ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O
ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H
ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H
ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O
ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H
ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H
ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O
ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H
ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H
ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O
ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H
ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H
ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O
ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H
ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H
ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O
ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H
ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H
ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O
ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H
ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H
ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O
ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H
ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H
ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O
ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H
ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H
ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O
ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H
ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H
ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O
ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H
ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H
ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O
ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H
ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H
ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O
ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H
ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H
END

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# file "spce.lt"
#
# H1 H2
# \ /
# O
SPCE {
write_once("In Init") {
# -- Default styles (for solo "SPCE" water) --
units real
atom_style full
# (Hybrid force fields were not necessary but are used for portability.)
pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
bond_style hybrid harmonic
angle_style hybrid harmonic
kspace_style pppm 0.0001
pair_modify mix arithmetic
}
write("Data Atoms") {
$atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
$atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
$atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
}
write_once("Data Masses") {
@atom:O 15.9994
@atom:H 1.008
}
write("Data Bonds") {
$bond:OH1 @bond:OH $atom:O $atom:H1
$bond:OH2 @bond:OH $atom:O $atom:H2
}
write("Data Angles") {
$angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
}
write_once("In Settings") {
bond_coeff @bond:OH harmonic 1000.0 1.0
angle_coeff @angle:HOH harmonic 1000.0 109.47
pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166
pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058
group spce type @atom:O @atom:H
fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
# (Remember to "unfix" fShakeSPCE during minimization.)
}
} # end of definition of "SPCE" water molecule type

16
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import "spce.lt"
wat = new SPCE [260]
# Open up the PDB file to count the number of water molecules inside. (Or just
# divide the number of atoms by 3). Put that in between the brackets ("[260]")
#
# The command above does not set the positions of the atoms.
# So they will have to be loaded later from a PDB or an XYZ file.
# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt")

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# PREREQUISITES:
#
# You must use moltemplate.sh to create 3 files:
# system.data system.in.init system.in.settings
# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
read_data system.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# -- minimization protocol --
# Note: The minimization step is not necessary in this example. However
# in general, it's always a good idea to minimize the system beforehand.
# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
unfix fShakeSPCE
minimize 1.0e-3 1.0e-5 100000 400000
# Now read "system.in.settings" in order to redefine fShakeSPCE again:
include system.in.settings
# -- simulation protocol --
timestep 1.0
dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
thermo 100
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
write_data system_after_npt.data

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tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt Normal file
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# PREREQUISITES:
#
# 1) You must use moltemplate.sh to create 3 files:
# system.data system.in.init system.in.settings
# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
# 2) You must equilibrate the system beforehand using "run.in.npt".
# This will create the file "system_after_npt.data" which this file reads.
# (Note: I have not verified that this equilibration protocol works well.)
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
# Read the coordinates generated by an earlier NPT simulation
read_data system_after_npt.data
# (The "write_restart" and "read_restart" commands were buggy in 2012,
# but they should work also. I prefer "write_data" and "read_data".)
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# -- minimization protocol --
# Note: If you are reading the data file created by run.in.npt,
# then you should not need to minimize the system beforehand.
# fShakeSPCE was defined in system.in.settings.
# (It is incompatible with "minimize".)
unfix fShakeSPCE
minimize 1.0e-5 1.0e-7 100000 400000
# Now read "system.in.settings" in order to redefine fShakeSPCE again:
include system.in.settings
# -- simulation protocol --
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
thermo 500
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
write_data system_after_nvt.data