-
Notifications
You must be signed in to change notification settings - Fork 0
/
qmmmpymbar
executable file
·159 lines (101 loc) · 2.52 KB
/
qmmmpymbar
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
#!/bin/bash
### MO 2015-03-01
#2 lam: 0.000 1.000
#3 lam: 0.000 0.500 1.000
#4 lam: 0.000 0.333 0.666 1.000
#5 lam: 0.000 0.250 0.500 0.750 1.000
#9 lam: 0.000 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.000
suffix="$1l"
makeresults2 () {
for x in prot wat ; do
for state in v0 ; do
for lambda_val in "0.000" "1.000" ; do
lam=$(echo $lambda_val | cut -c 1,3-5)
ambtombar<<EOI
$x-lam$lam-sander-$state.out4
mbar-mmscn-$suffix-$x.$lam
2
0.000 1.000
EOI
done
pymbar_alchemical.py mbar-mmscn-$suffix-$x 300 0 0.000 1.000 >mbar-results-$suffix-$x
done
done
}
makeresults3 () {
for x in prot wat ; do
for state in v0 ; do
for lambda_val in "0.000" "0.500" "1.000" ; do
lam=$(echo $lambda_val | cut -c 1,3-5)
ambtombar<<EOI
$x-lam$lam-sander-$state.out4
mbar-mmscn-$suffix-$x.$lam
3
0.000 0.500 1.000
EOI
done
pymbar_alchemical.py mbar-mmscn-$suffix-$x 300 0 0.000 0.500 1.000 >mbar-results-$suffix-$x
done
done
}
makeresults4 () {
for x in prot wat ; do
for state in v0 ; do
for lambda_val in "0.000" "0.333" "0.666" "1.000" ; do
lam=$(echo $lambda_val | cut -c 1,3-5)
ambtombar<<EOI
$x-lam$lam-sander-$state.out4
mbar-mmscn-$suffix-$x.$lam
4
0.000 0.333 0.666 1.000
EOI
done
pymbar_alchemical.py mbar-mmscn-$suffix-$x 300 0 0.000 0.333 0.666 1.000 >mbar-results-$suffix-$x
done
done
}
makeresults5 () {
for x in prot wat ; do
for state in v0 ; do
for lambda_val in "0.000" "0.250" "0.500" "0.750" "1.000" ; do
lam=$(echo $lambda_val | cut -c 1,3-5)
ambtombar<<EOI
$x-lam$lam-sander-$state.out4
mbar-mmscn-$suffix-$x.$lam
5
0.000 0.250 0.500 0.750 1.000
EOI
done
pymbar_alchemical.py mbar-mmscn-$suffix-$x 300 0 0.000 0.250 0.500 0.750 1.000 >mbar-results-$suffix-$x
done
done
}
makeresults9 () {
for x in prot wat ; do
for state in v0 ; do
for lambda_val in 0.000 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.000 ; do
lam=$(echo $lambda_val | cut -c 1,3-5)
ambtombar<<EOI
$x-lam$lam-sander-$state.out4
mbar-mmscn-$suffix-$x.$lam
9
0.000 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.000
EOI
done
pymbar_alchemical.py mbar-mmscn-$suffix-$x 300 0 0.000 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.000 >mbar-results-$suffix-$x
done
done
}
if [ "$1" = "2" ] ; then
makeresults2
elif [ "$1" = "3" ] ; then
makeresults3
elif [ "$1" = "4" ] ; then
makeresults4
elif [ "$1" = "5" ] ; then
makeresults5
elif [ "$1" = "9" ] ; then
makeresults9
else
echo "Error in use of script."
fi