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[ESPResSo] Re: analyze nbhood & Bond-angle Interactions

From: Peter Kosovan
Subject: [ESPResSo] Re: analyze nbhood & Bond-angle Interactions
Date: Tue, 23 Oct 2007 12:49:30 +0200 (CEST)

Dear Lorenzo

In my opinion, using the bond-angle potential to represent non-spherical shape and angle-dependent interactions in the aggregation of colloidal particles is not the most natural choice. Moreover, using the FENE-type of bond for a colloidal system seems wierd to me as well. I would suggest a different workaround.

First of all, I would suggest using lennard-jones type of a potential between the particles should suffice to stick them together rather than introducing a true bond between them. If you set epsilon_LJ>>kT, then once the particles find each other, they stick together. If you set epsilon_LJ comparable to kT, you also get a finite probability that a particle escapes from the cluster which seems to me a more physical picture of a colloidal system when compared to introducing non-breakable FENE bonds.

The second suggestion is that you do not have to represent a single colloidal particle by a single particle in Espresso. In the simplest case, you can represent it by two espresso-particles forming a dumbbell (dimer), or you can build more complicated representations such as A-B-A trimer, with the A-B-A bond angle fixed. In this way, a colloidal particle of any shape can be represented and the individual espresso-particles play the role of interaction sites on the surface of the colloidal particle.

With regards


Peter Kosovan
Department of Physical and Macromolecular Chemistry
Faculty of Science
Charles University in Prague
Czech Republic
Tel. +420 221 951 290

On Tue, 23 Oct 2007, address@hidden wrote:

Date: Tue, 23 Oct 2007 12:00:09 +0200
From: address@hidden
Reply-To: address@hidden
To: address@hidden
Subject: ESPResSo Digest, Vol 5, Issue 12

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Today's Topics:

  1. RE: Fwd: analyze nbhood & Bond-angle Interactions
     (Limbach, Hans Joerg, LAUSANNE,    NRC-FS)


Message: 1
Date: Mon, 22 Oct 2007 13:52:05 +0200
From: "Limbach, Hans Joerg, LAUSANNE,      NRC-FS"
Subject: RE: [ESPResSo] Fwd: analyze nbhood & Bond-angle Interactions
To: "Lorenzo Isella" <address@hidden>,
Content-Type: text/plain;       charset="us-ascii"

Dear Lorenzo,

(1) A bond (or dihedral) angle potential should always be used in
connection with two body bond potentials which will set the interaction
range. E.g. if you place a bond angle between the particles 0, 1 and 2
(1 being the middle particle) you schoud set bonds between the particles
0 and 1 and between 1 and 2. Otherwise Espresso will crash at some
(2) nbhood does not give the particles in a specific order. I mentioned
it to you since I thought nbhood could be a starting point to solve your
problem. After you got the list you have to find out on the tcl level
how the particles are arranged towards each other.

Best regards,

-----Original Message-----
From: address@hidden
[mailto:address@hidden On Behalf Of
Lorenzo Isella
Sent: vendredi, 19. octobre 2007 17:38
To: address@hidden
Subject: [ESPResSo] Fwd: analyze nbhood & Bond-angle Interactions

Dear All,
Thanks for the very useful bits of advice I got on the list.
I am now running some experiments with really simple systems,
made up of 3 particles.
The idea is how suggested on this list: when particles get
"close enough", I stick them together with a potential which
depends on the angle (a rigid bond).
I have a few questions for the list.
(1) if I look at Eq. 5.16 of the Espresso manual
(bond_angle_cosine) I do not see how the length of the bond
is defined. I mean: the particles will have a preferred
orientation but what is the range of the interaction? Can I
specify it?
(2) the command analyze nbhood  tells me how many particles I
have within a given distance from a certain particle. It
returns a list of particle numbers, but what is the meaning
of the order in which the numbers appear? I mean, say I am
looking for the particles surrounding particle 1 and I get
the array 0 1 2. Does that tell me anything about which
particle is in the middle?
Particles 0 and 2 could be on the same side wrt particle 1,
or particle 1could be somewhere in between. This is important
seen that I need to know which is the central particle to set
up the bond-angle interaction.
(3)In the end it all boils down to the problems I am
experiencing in setting up a system with a few particles able
to interact via a bond-angle interaction.
In the code below, everything should work (in the end I check
that my particle 1 has the bonded interaction), but from VMD
that does not seem to be the case...


set n_part 3; set density 0.007
set box_l [expr pow($n_part/$density,1./3.)]

setmd box_l $box_l $box_l $box_l
setmd periodic 1 1 1

inter 0 angle 700.0 0.8
set q 0; set type 0

# I now set the particle charge to 0 and see if the code
works the same of not

for {set i 0} { $i < $n_part } {incr i} { set posx [expr
$box_l*[t_random]] set posy [expr $box_l*[t_random]] set posz
[expr $box_l*[t_random]] part $i pos $posx $posy $posz q $q
type $type }

puts "[part ]"

setmd time_step 0.01; setmd skin 0.4
set temp 0.0005; set gamma 0.01
thermostat langevin $temp $gamma
set integ_steps 200
set vmd "yes"

if { $vmd == "yes" } {
    prepare_vmd_connection tutorial 3000
    exec sleep 4
    imd positions

set activate_fene 1
set fene_warning 1
set integ_step 20

for {set i 0} { $i < 2000 } { incr i} {
set temp [expr [analyze energy kinetic]/(1.5*$n_part)] #puts
"t=[setmd time] E=[analyze energy total], T=$temp"
integrate $integ_steps

if { $vmd == "yes" } { imd positions }
set acti [analyze nbhood 1 4.5]

set neighbor [analyze nbhood 1 4.]
#puts " the neighbors are, $neighbor "
set mylen [llength $neighbor]

if { $mylen == 3 && $activate_fene == 1 } {

part 1 bond 0 0 2
puts "activated angle bond!"
set activate_fene 0

puts "[part ]"

puts "So far so good"

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