Hi,
I am simulating a confined fluid of particles interacting through the repulsive part of the LJ potential.
To confine the system i am using the cylinder constraint implemented in ESPRessSo (Ver. 3.1), however i facing some troubles.
In the initial configuration my 625-particles (diam_col = 0.4) are located along the x-axis without overlapping
Part: 618 pos: 618.5 312.5 312.5
Part: 619 pos: 619.5 312.5 312.5
and the cylinder is defined as
0 cylinder center 312.5 312.5 312.5 axis 1.0 0.0 0.0 radius 0.42 length 312.5 direction -1.0 type 1 penetrable 0
a)
My first problem is related with the radius of the cylinder.
With the actual value of radius (0.42), the simulation runs fine but the particles seem (in vmd) to be very confined, i.e., it does not appear that particles are inside a cylinder of
diameter 0.84 (2.1*diameter_col).
If I decrease slightly the radius value, say radius 0.4 => cylinder diameter 0.8 => (2.0*diam_col) then the simulation crash immediately and I do not understand why?
If understand well the cylinder has a diameter that is twice the particles diameter. This diameter should be enough for particles to move along the channel.
Could you help me to clarify this point.
b) My second problem is related with the visualization of the constraint in vmd. I follow the
tutorial.tcl script included in espresso.
if {$vmd == "yes"} {
prepare_vmd_connection cilindro start wait 3000 constraints
imd positions
}
Then inside the cycle
if { $vmd == "yes" } { imd positions }
With these commands in my script, I am able to launch vmd and visualize the particles but I can not visualize the cylinder. I was wondering what I missing or what I am doing wrong.
Any help would be greatly appreciated.
Thanks a lot in advance
salvador
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