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
|
<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>CG-CG</name>
<!-- types involved in this interaction -->
<type1>CG</type1>
<type2>CG</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.24</min>
<max>0.9</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromacs rdf.xvg -->
<target>CG-CG.dist.tgt</target>
<!-- this is for analysis only -->
<!--density>
<target>dens_CG_CG_aim.xvg</target>
<min>0</min>
<max>10.8</max>
<step>0.2</step>
</density-->
<!-- update cycles -->
<do_potential>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_CG_CG.xvg</table>
</gromacs>
<optimizer>
<target_weights>10 0.01</target_weights>
<function>f(x)</function>
<functionfile>function_CKDg.in</functionfile>
<parameters>sig eps wc h p s</parameters>
<targets>rdf pressure</targets>
<rdf>
<target>CG-CG.dist.tgt</target>
<weight>f(x)</weight>
<weightfile>function_rdf_weight.in</weightfile>
</rdf>
</optimizer>
<p_target>1.0</p_target>
</inverse>
</non-bonded>
<inverse>
<!-- general options for inverse script -->
<initial_configuration>maindir</initial_configuration>
<!-- 300*0.00831451 gromacs units -->
<kBT>2.49435</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<pre_simulation>yes
<mdp>grompp.prep.mdp</mdp>
</pre_simulation>
<!-- 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>3.0</table_end>
<log>gromacs.log</log>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.prep.mdp grompp.mdp topol.top table.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>900</iterations_max>
<!-- ibm: inverse boltzmann imc: inverse monte carlo -->
<method>optimizer</method>
<optimizer>
<!-- put simplex or cma here -->
<type>simplex</type>
<cma>
<eps>0.1</eps>
</cma>
</optimizer>
</inverse>
</cg>
|
