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Re: [ESPResSo-users] Constrainst visualization


From: Georg Rempfer
Subject: Re: [ESPResSo-users] Constrainst visualization
Date: Sun, 15 Nov 2015 13:41:51 +0100

Hello Salvador,

what you describe is definitely a bug. Unfortunately, I don't have time to look into in right now. You are right, the visualization of the constraints in VMD and the simulation are completely separate. I am certain that this does not affect the simulation.

The constraint visualization is a simple TCL function in the scripts folder. Check out the "prepare_vmd_connection" function in "scripts/auxiliary.tcl". The interesting part for you starts at line 365 with "if {$draw_constraints != "0"} {". This might be quite easy to fix. If you manage, send us a pull request on Github or contact me. If you don't manage but have a suspicion, tell us here.

Greetings,
Georg

On Wed, Nov 11, 2015 at 7:49 PM, Salvador H-V <address@hidden> wrote:
Hi,

First to all, I want to thanks Georg  and Axel by their suggestions and comments that help me to solve the troubles of my last post.

What I have found is thtat, when I use a comand with something like this
constraint cylinder center 0.0 0.0 0.0 axis 1 0 0 radius 0.42 length 5 direction inside type 0
prepare_vmd_connection test wait 2000 constraints

Espresso creates a file: test.vmd.script where the instructions to draw the cylinder area as follows:
draw cylinder {-5.0 0.0 0.0} {5.0 0.0 0.0} radius 0.42 resolution 36
Which draws a cylinder in an expected location

But if the center is not in  (0,0,0) the draw cylinder instruction are modified in someway that I do not understand.
For example using:
constraint cylinder center 10.0 0.0 0.0 axis 1 0 0 radius 0.42 length 5 direction inside type 0
prepare_vmd_connection test wait 2000 constraints

I was expecting a cylinder of length 10 whit initial coordinates (5, 0, 0) and end coordinates
(15,0,0), but what I got was...
draw cylinder {45.0 0.0 0.0} {55.0 0.0 0.0} radius 0.42 resolution 36

I do not where the coordinates come from. So, in my simulations I have a cylinder of length of 625 which is drawn with very far coordinates.

Anyway, right now I am able to "move" the cylinder to the right position and I can visualize the particles inside the cylinder.

Finally, I have to questions:
a) Just to be on the safe side, the visualization and the way that Espresso manage the channel-particle interaction are independently, right? I mean, I do not have to be worried that the channel-visualization is not in the right position.

b) It is possible to change the cylinder graphic properties, I would like to visualize a transparent/Ghost cylinder.  I tried directly in vmd with no success.

Any suggestion would be greatly appreciated

Thanks a lot in advance

Salvador    

 
 

 


 

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