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
|
<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>A-A</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>A</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.31</min>
<max>1.36</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromacs rdf.xvg -->
<target>A-A.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_A.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>B-B</name>
<!-- types involved in this interaction -->
<type1>B</type1>
<type2>B</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.31</min>
<max>1.38</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromacs rdf.xvg -->
<target>B-B.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 1 0</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_B_B.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<!-- name of the interaction -->
<name>A-B</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>B</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.31</min>
<max>1.36</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromacs rdf.xvg -->
<target>A-B.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_B.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- 200*0.00831451 gromacs units -->
<kBT>1.66290</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>20</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.002</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>2.5</table_end>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg table_a1.xvg table_b1.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibi: inverse boltzmann imc: inverse monte carlo -->
<method>ibi</method>
<!-- directory for user scripts -->
<scriptpath>$PWD</scriptpath>
<!-- write log to this file -->
<log_file>inverse.log</log_file>
<!-- write restart step to this file -->
<restart_file>restart_points.log</restart_file>
<!-- imc specific stuff -->
</inverse>
</cg>
|
