|
From: | Georg Rempfer |
Subject: | Re: [ESPResSo-users] Help with cylinder constraint |
Date: | Sat, 7 Nov 2015 00:02:35 +0100 |
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 filecilindro.vmd_start.script I have the following lines:logfile vmd.logmol load vsf cilindro.vsfrotate stopmol modstyle 0 0 CPK 1.800000 0.300000 8.000000 6.000000mol modcolor 0 0 Nameimd connect localhost 10000imd transfer 1imd keep 1draw color graydraw cylinder {97343.75 0.0 0.0} {97968.75 0.0 0.0} radius 0.42 resolution 36and in the filecilindro.vsf i have only the linespbc 625.0 625.0 625.0atom 0:624 radius 0.25 name O type 0 q 0.0I 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 advanceSalvadorOn 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 0prepare_vmd_connection test wait 2000 constraintsdraws 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 overlappingPart: 618 pos: 618.5 312.5 312.5Part: 619 pos: 619.5 312.5 312.5and the cylinder is defined as0 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 0a)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 ofdiameter 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 thetutorial.tcl script included in espresso.if {$vmd == "yes"} {prepare_vmd_connection cilindro start wait 3000 constraintsimd positions}Then inside the cycleif { $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 advancesalvador--
cylinder.tcl
Description: Tcl script
test.vmd_start.script
Description: Binary data
[Prev in Thread] | Current Thread | [Next in Thread] |