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Re: [ESPResSo-users] analyze aggregation command


From: Axel Arnold
Subject: Re: [ESPResSo-users] analyze aggregation command
Date: Thu, 12 Jun 2014 15:58:58 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Thunderbird/24.5.0

Hi!

Unfortunately, Espresso has several different ways of storing topology
info for historical reasons, and which are not necessarily in sync. In
your case, the analyze aggregation command relies on the mol_id property
of the particle, which is not set automatically. You can either set the
mol_id yourself, or you use "analyze set topo_part_sync" to transfer the
information from the molecules to the particles after the analyze set
chains.

Best,
Axel

On 06/08/2014 09:46 AM, Narges Nikoofard wrote:
> 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


-- 
JP Dr. Axel Arnold
ICP, Universit├Ąt Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609




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