Re: [ESPResSo] aggregation

[Tristan Bereau]

Salut Guillaume,

I don't know what your parameters look like, but the box size could be
too small (although as there are no units, it's just a wild guess!). If
I were you I'd try a simulation with only 2 polymer chains, redo the
aggregation analysis, and on top of that look at the output using PDB files.

Best,
Tristan

Guillaume Larsen wrote:
> Hi Mehmet,
>
> thanks for replying!
>
> The system I test contains 20 polymer chains of 10 monomers each in a
> cubic box of length equals 10, which is small enough I think.
> I have changed several simulation parameters, but still the same kind
> of output.
>
> Guillaume
>
> > Date: Wed, 21 Apr 2010 09:23:04 +0300
> > From: address@hidden
> > To: address@hidden
> > CC: address@hidden
> > Subject: Re: [ESPResSo] aggregation
> >
> > Hi,
> >
> > The output gives the maximum, minimum, average aggregate sizes. The
> > standard deviation of the distribution, the number of aggregates, and
> > finally a list of list where one can find which particles belong to
> > which aggregate.
> > This is printed out for each frame processed.
> >
> > Looking at the output you send, the results don't really make much
> sense.
> > The maximum aggregate size seems extremely large, and the standard
> > deviation calculation has failed for some reason.
> >
> > How many particles do you have in the system?
> > I would try this routine on a small system first.
> >
> > You would need to process this output and obtain the aggregate size
> > distribution with a separate routine.
> >
> > Mehmet
> >
> > Guillaume Larsen wrote:
> > > dear all,
> > >
> > > I am trying to use the 'analyze aggregation' command.
> > > The output of this function is not really clear to me.
> > > It is supposed to return the aggregate size distribution for the
> > > molecules (as explained in the user's guide), however in my procedure
> > > this function returns something like:
> > > MAX 397749225 MIN 1 AVG 79549840.000000 STD nan AGG_NUM 5 AGGREGATES
> > > { 1 } { 2 } { 3 } { 4 } { 5 }
> > > MAX 397749225 MIN 1 AVG 79549840.000000 STD nan AGG_NUM 5 AGGREGATES
> > > { 1 } { 2 } { 3 } { 4 } { 5 }
> > > MAX 397749225 MIN 1 AVG 79549840.000000 STD nan AGG_NUM 5 AGGREGATES
> > > { 1 } { 2 } { 3 } { 4 } { 5 }
> > > (...)
> > > What is the meaning of this output? And actually how to directly
> > > obtain the aggregate size distribution of molecules?
> > >
> > > Thank you in advance for your help.
> > >
> > > Regards,
> > >
> > > Guillaume
> > >
> > >
> ------------------------------------------------------------------------
> > > Hotmail débarque sur votre téléphone ! Paramétrez Hotmail sur votre
> > > téléphone! Gratuit !
> <http://www.messengersurvotremobile.com/?d=Hotmail>
> > >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > ESPResSo mailing list
> > > address@hidden
> > > https://fias.uni-frankfurt.de/mailman/listinfo/espresso
> > >
>
> ------------------------------------------------------------------------
> Commander un cadeau en ligne discrètement? Voir la solution offerte
> par Internet Explorer8 <http://clk.atdmt.com/FRM/go/207186971/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> ESPResSo mailing list
> address@hidden
> https://fias.uni-frankfurt.de/mailman/listinfo/espresso
>