[ESPResSo-users] analyze aggregation command

[Narges Nikoofard]

Dear all,

I am simulating a system of amphiphilic polymers. I want to use the "analyze aggregarion" command to track aggregates.

When I have 10 polymers, each with 20 monomers, I define the molecules like this:
analyze set chains 0 10 20
puts [analyze set]

This is the output of the second line:
{ 0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 } { 0 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 } { 0 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 } { 0 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 } { 0 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 } { 0 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 } { 0 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 } { 0 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 } { 0 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 } { 0 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 }

Then I try to use the analyze aggregation command to track the aggregates:
puts $file [analyze aggregation 4.0 0 9]

The simulation goes well and I see in VMD that three aggregates with 3-4 monomers exist. But the output in the $file shows no aggregation. All through the $file, this line is repeated:
MAX 1 MIN 1 AVG 1.000000 STD 0.000000 AGG_NUM 10 AGGREGATES { 0 }  { 1 }  { 2 }  { 3 }  { 4 }  { 5 }  { 6 }  { 7 }  { 8 }  { 9 }
 

I have performed the simulation in different conditions, but I get a similar file with no aggregates, every time.

I wonder if I have understood and used the command correctly. I use Espresso 3.2.0. I would be grateful if someone could kindly help me in this issue.

Many thanks in advance,

Narges Nikoofard