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Re: [ESPResSo-users] find aggregates

From: Narges Nikoofard
Subject: Re: [ESPResSo-users] find aggregates
Date: Sat, 27 Jun 2015 11:23:48 +0430

Dear Dr. Kosovan,

Many thanks for the ideas about the time and length scales in studying self-assembly. They were really useful for me. About the bug in the implementation, what can I do? I am thinking about writing a tcl code for this myself. Is there any other way?

Dear Dr. Brunel,

Many thanks for the note. I think that solitary molecules in the solution should also be counted as independent aggregates. Also, total number of molecules in the two given aggregates by the command is equal to the total number of molecules in the system, which is not compatible with visual inspection. The other thing is that it gives two molecules in one of the aggregates which is not correct too. I wonder if my reasoning is correct and these are not the real aggregates.

Many thanks again,
Narges Nikoofard

On Thu, Jun 25, 2015 at 5:39 PM, Fabrice Brunel <address@hidden> wrote:

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.


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

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