Re: [ESPResSo-users] Constrainst visualization

[Axel Arnold]

Forgot reply all... But since Georg just answered, wanted to repeat that the 
error rather looks like a script problem, see below.

Axel

> Hi!
> 
>> Am 11.11.2015 um 19:49 schrieb Salvador H-V <address@hidden>:
>> 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
> 
> That sounds like you first add the constraint, then set the box length, and 
> then draw the cylinder. Espresso stores coordinates as multiples of the box 
> length + remainder. If you put the cylinder at 10 in a 1-box, that is in fact 
> a 10L+0. When you resize to a 5-box, you get 10*5 = 50 as center, and voila.
> 
> 
>> 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.
> 
> Not quite, as explained above.
> 
>> 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.
> 
> You can do that by setting the material in vmd. I don’t remember quite how, 
> but there was something like graphics material Transparent.
> 
> Best,
> Axel
>