Re: [ESPResSo-users] find aggregates

[Fabrice Brunel]

Hi,

I think the "analyze aggregation" command require that you setup a mol_id for each molecule.

I ran your code after adding this :

for {set i 0} {$i < $N} {incr i} {
   for {set j 0} {$j < [expr $N1+$N2]} {incr j} {
      part [expr $i*($N1+$N2)+$j] mol $i
   }
}

It gives 2 aggregates with the distance criteria 1.5 and 2.0 which is compatible with the visual inspection.

Hope it helps.

Fab

2015-06-24 14:03 GMT+02:00 Narges Nikoofard <address@hidden>:

Dear all,

I am studying the self-assembly of amphiphilic polymers. I use the "analyze aggregation" command to find the aggregates.

Although I see in VMD that there are several free polymers and two micelles in the system, the command gives all molecules in one aggregate. I have checked different values for dist_criteria.

The code is attached to this email. I would be grateful if someone could kindly help me in this issue.

Many thanks in advance,

Narges Nikoofard