Re: [ESPResSo-users] Help with cylinder constraint

[Salvador H-V]

Hi Georg,

Thanks a lot for your answer. 

Your command and the one I am using are very similar. In my case I choose axis 1 0 0 because I want a cylinder along the x-axis. Is this correct?

I tried with your command but still I can see in vmd only the particles but no the cylinder. In fact, in the file 

cilindro.vmd_start.script  I have the following lines:

logfile vmd.log

mol load vsf cilindro.vsf

rotate stop

mol modstyle 0 0 CPK 1.800000 0.300000 8.000000 6.000000

mol modcolor 0 0 Name

imd connect localhost 10000

imd transfer 1

imd keep 1

draw color gray

draw cylinder {97343.75 0.0 0.0} {97968.75 0.0 0.0} radius 0.42 resolution 36

and in the file 

cilindro.vsf i have only the lines

pbc 625.0 625.0 625.0

atom 0:624 radius 0.25 name O type 0 q 0.0

I was wondering if this format is correct. Besides,  I would like to ask you for a basic script in order to corroborate that I am able to see the cylinder.

Thanks a lot in advance

Salvador

On Thu, Nov 5, 2015 at 12:07 PM, Georg Rempfer <address@hidden> wrote:

b) constraint cylinder axis 1 1 1 length 5 radius 1 center 0 0 0 direction outside type 0

    prepare_vmd_connection test wait 2000 constraints

draws a cylinder for me.

On Thu, Nov 5, 2015 at 5:38 PM, Salvador H-V <address@hidden> wrote:

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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