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From: | Georg Rempfer |
Subject: | Re: [ESPResSo-users] Constrainst visualization |
Date: | Sun, 15 Nov 2015 13:41:51 +0100 |
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 thisconstraint cylinder center 0.0 0.0 0.0 axis 1 0 0 radius 0.42 length 5 direction inside type 0prepare_vmd_connection test wait 2000 constraintsEspresso 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 36Which draws a cylinder in an expected locationBut 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 0prepare_vmd_connection test wait 2000 constraintsI 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 36I 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 appreciatedThanks a lot in advanceSalvador-
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