Dear Users,<br>
<br>
I have molecule types Ions and Sol in my system. Sol has 124 OX
atoms with residue name MY. Ions has 1 C atom with res name DP. My
index file [ Ions ] 1 and [ Sol ] 2 to 125.<br>
I use user defined potentials for Ions and Sol. I write energygrps =
Ions Sol and energygrp_table = Ions in my .mdp file. I am trying to
freeze Sol using freeze groups. Its a NVE simulation. I am not using
constraints. I am not using energygrp_excl. I am using 2 table files
table.xvg and table_Ions.xvg.<br>
<br>
I give the system an initial velocity at a temp of 90 K. Sol
should not move and it doesnt. However in my case Ions is not moving
too.<br>
<br>
Any clue why is this happening? Have I used wrong group names in
any of the files? Could something be wrong with my potential table
files? Any sort of help is welcome.<br>
<br>
Thanks in advance.<br>
<br>
Karamyog Singh,<br>
Undergraduate student,<br>
IIT Kharagpur,<br>
India.<br>
<br>
My out.gro file looks like this: <br>
<br>
<br>
What is wrong<br>
125<br>
1DP C 1 12.000 12.000 6.000<br>
2MY
OX 2 0.000 0.000
6.000<br>
3MY OX 3 0.000 0.000 12.000<br>
4MY OX 4 0.000 0.000 18.000<br>
5MY OX 5 0.000 0.000 24.000<br>
6MY
OX 6 0.000 6.000
0.000<br>
7MY
OX 7 0.000 6.000
6.000<br>
8MY OX 8 0.000 6.000 12.000<br>
9MY OX 9 0.000 6.000 18.000<br>
...............................<br>
<br>
<br>
My index.ndx file is like this:<br>
<br>
[ Ions ]<br>
1<br>
<br>
[ Sol ]<br>
2 3
4 5 6
7 8 9 10
11 12 13 14
15 16<br>
17 18 19 20
21 22 23 24
25 26 27 28
29 30 31<br>
32 33 34 35
36 37 38 39
40 41 42 43
44 45 46<br>
47 48 49 50
51 52 53 54
55 56 57 58
59 60 61<br>
62 63 64 65
66 67 68 69
70 71 72 73
74 75 76<br>
77 78 79 80
81 82 83 84
85 86 87 88
89 90 91<br>
92 93 94 95
96 97 98 99 100
101 102 103 104 105 106<br>
107 108 109 110 111 112
113 114 115 116 117 118 119
120 121<br>
122 123 124 125<br>
<br>