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Re: [ESPResSo-users] Constrainst visualization
From: |
Axel Arnold |
Subject: |
Re: [ESPResSo-users] Constrainst visualization |
Date: |
Mon, 16 Nov 2015 13:26:57 +0100 |
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
>