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Re: [ESPResSo-users] find aggregates

From: Peter Košovan
Subject: Re: [ESPResSo-users] find aggregates
Date: Thu, 25 Jun 2015 14:35:39 +0200

Hi Narges,

I have not used [analyze aggregation] before, but tried a simple test. See your script - modified and attached.

Looking at the output files with the distance criteria 1.0, 1.5 and 2.0, obviously the result is not always a single aggregate. But it is very sensitive to the distance and none of these results is compatible with the visual inspection, which gives 2 aggregates plus a number of free chains (each of them is counted as an "aggregate" by itself). This could indicate a possible bug in the implementation, but I have not had time to check the code.

Please be aware that for a meningful simulation of aggregation, you need to simultaneously satisfy two things:
1. average aggregation number much smaller than the number of chains per box (rule of thumb >10 aggregates per box), otherwise you get strong finite size effects
2. simulation runtime much longer (rule of thumb > 100times) than the timescale of the exchange of chains between different aggregates. Otherwise you can't be sure whether you are not simulating a metastable state. This time scale drastically increases with aggregate size and LJ epsilon.

I am afraid that meeting these criteria with Langevin dynamics will be a tough job.

Best regards,


On Wed, Jun 24, 2015 at 2:03 PM, Narges Nikoofard <address@hidden> wrote:
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

Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze
Tel. +420221951290
Fax +420224919752

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Attachment: amphiphiles_mod.tcl
Description: Tcl script

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