Hello Christoph,
Your suggestion sounds really interesting.
I still doubt that it can be useful in a simulation starting with
individual monomers (basically, I do not know which aggregates I am
generating while evolving the system; this is done when
post-processing the results and looking at the individual positions of
all the monomers).
Nevertheless, I think that your suggestion would help me a lot when
studying the aggregate diffusion properties.
In that case, I already select an aggregate generated from a previous
simulation, make many copies of it and put all of them in the middle
of a box. Since I consider the i-th cluster as consisting of monomers
of the i-th type only, and there is no interaction between monomers of
the i-th and j-th type, two distinct clusters are "transparent" to
each other and I can track plenty of them simultaneously.
I can now do something similar with the inter_dpd.
Some questions:
(1) In setting up the interaction:
inter X Y inter_dpd GAMMA CUTOFF WF TGAMMA TCUTOFF TWF
what do GAMMA CUTOFF WF TGAMMA TCUTOFF TWF stand for?
Are GAMMA CUTOFF WF, the damping, cut-off and the noise strength as
for for the DPD thermostat, but only for particles of type X?
Are the quantities starting with "T" the same for particles of type Y?
Is there any reference paper?
(2) Do I need to stop the centre-of-mass motion before setting up this
thermostat? I refer to the galileiTransformParticles, which is not
documented in detail in the user guide.
Many thanks
Lorenzo
Date: Fri, 05 Sep 2008 11:20:00 +0200
From: Christoph Junghans <address@hidden>
Subject: Re: [ESPResSo] Questions about Thermostat
To: Lorenzo Isella <address@hidden>
Cc: address@hidden
Message-ID: <address@hidden>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear Lozenro,
Torsten's answer was not 100% correct. There is the (so far
undocumented) inter_dpd, which allows you to use different frictions for
different particle types.
######### BEGIN technical details#######
use #define INTER_DPD in myconfig.h
set thermostat inter_dpd TEMP
inter X Y inter_dpd GAMMA CUTOFF WF TGAMMA TCUTOFF TWF
######### END technical details#########
The only problem here is: How do distinguish between different
aggregates? By particle type?
Because inter_dpd uses particle types to decide what to do.
(Btw. changing the particle type of fly is not a good idea for mpi.)
Cheers,
Christoph
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