I've been able to nicely install MEMB plugin on OSx and PC's but following the same directions, the plugin fails to appear in VMD Extensions> Analysis installed in Linux Ubuntu ( where the MD files are located ) Is there an additional step/s for linux installation ?
thanks
pb
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Dear Paul, installation instructions in https://sourceforge.net/p/membplugin/wiki/Installation/ have been tested on linux. Please, read carefully and follow those instructions. Then, if you are still experiencing problems don't hesitiate to contact us.
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Thank you for the prompt response. I've tried to be very careful about the installation , and installation for linux seems to be the same as that for OS X and Win which work as described- the demos run nicely. Barring some quirk of Linux Mint ( I've got VMD, and Schrodinger working on the same machine ) then I am missing something obvious. It's not for lack of trying - two different Lixux machines behave similarly .
In the meantime is there a command line workaround ?
thanks
Paul
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pb@MSI ~ $ vmd
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a9 (October 19, 2017)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd@ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 15GB (96%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: GeForce GTX 970/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU...
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
vmd > busce004@umn.edu
I noticed that MEMB does not recognize the CUDA. But it is installed: nvcc - V does gives the version -9 , and Schrodinger/Desmond sees the GPU as well
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With the information that you provided, it is very likely that you have two VMD installs in your computer:
one in /usr/local/lib/vmd/ with 1.9.4a9 VMD version and another one in /home/pb/Desktop/vmd-1.9.3.
Please, check that you are installing the pluging in the same VMD that you run afterwards and modify your PATH variable in .bashrc accordingly for convenience.
Furthermore, installation has not been tested on VMD 1.9.4a9, and MEMBPLUGIN does not use CUDA, so CUDA errors are probably not related with your issue.
Last edit: Ismael Rodriguez Espigares 2017-11-30
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What you say is correct, there were two versions. But MEMB did not appear with either v3 or v4 of VMD.
In any event, is there perhaps an alternate command line method of accessing the plugin ?
thanks
Paul
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OK.
Please, run again VMD (preferably version 1.9.3) in a terminal and open a TK console (Extensions --> TK Console) . Then, run the following commands in the TK Console and paste here any output printed in the TK console or in the linux terminal after running those commands. Paste also the commands with the actual paths that you used:
puts $env(VMDDIR); # this 'VMDDIR' is literal, do not replace
lappend auto_path /path/to/membplugin-release-1.x/membplugin1.x; # is a directory
source /path/to/membplugin-release-1.x/loadmembplugin.tcl; # is a file
Replace /path/to/membplugin-release-1.x/ with the path to the folder extracted from the release .zip file ("membplugin-release-1.x", membplugin-release-1.1 for membplugin-release-1.1-RC2.zip) and the "x" in membplugin1.x by the current MEMBPLUGIN minor version ("membplugin1.1" for membplugin-release-1.1-RC2.zip). The paths that you write must exist.
lappend auto_path command is crucial to make the plugin working, but we cannot know if it is working correctly until the package is loaded. So, you can try this command:
package require membplugin
to load a minimal package to have at least command-line access (no gui). If this command gives an error in the TK console or in the terminal copy and paste it in the forum.
Main< (pb) 5 % membranescd
Usage: membranescd -structure file -trajectory file [options]
Arguments:
-sel "atomselection" -- atom selection to be analysed (string).
Default: not resname CHL1
-lipid "resname1 resname2 ..." -- list of lipid resnames.
Default: $lipids in config.tcl file.
-chain {1 2 3} -- acyl chains to be analysed (list).
Default: {1 2 3}
-leaf {0 1} -- membrane leaflets to be analysed (list).
Default: {0 1}
-from -- init frame (integer or string). Default: 0
-to -- last frame (integer or string). Default: {last}
-step <int> -- frame step (integer). Default: 1
Other options:
-wrapcmd {command} -- command executed to wrap system up (string).
Default: {pbc wrap -center bb -centersel membplugin_lipid
-compound res -all}
-o <file> -- path to output file (string).
Default file path: loaded trajectory.
Default file extension: ".orderparSCD</file></int>
Main< (pb) 7 % lipidarea
Usage: membranescd -structure file -trajectory file [options]
Arguments:
-triatom {{"resnames" {atom1 [atom2 atom 3]}} ... }
-- resname and corresponding atom triad or single atom (list).
Default {{"DPPC DSPC DOPC SDPC" "C2 C21 C31"} {"SM18" "C2 C21 C3"} {"CHL1" "C13 C10"}}
-nodefaults -- ignore the default resnames and atom triads
-leaf {0 1} -- membrane leaflets to be analysed (list).
Default: {0 1}
-from -- init frame (integer or string). Default: 0
-to -- last frame (integer or string). Default: {last}
-step <int> -- frame step (integer). Default: 1
Other options:
-wrapcmd {command} -- a command that will be executed on each frame in order to wrap
the system. Default: {pbc wrap -center bb -centersel membplugin_lipid
-compound res -all}
-qvoronoi <path> -- path to the qvoronoi binary. If empty, the path in
config.tcl will be used.
-o <file> -- path to output file (string).
Default file path: loaded trajectory.
Default file extensions: "_average.area" and "_total.area"</file></path></int>
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Yes, that is the expected output. The only thing is that it is highly recommended to add only absolute paths (begining with backslash "/") when using "lappend auto_path" command as changing the working directory could make the packages stop working.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I've been able to nicely install MEMB plugin on OSx and PC's but following the same directions, the plugin fails to appear in VMD Extensions> Analysis installed in Linux Ubuntu ( where the MD files are located ) Is there an additional step/s for linux installation ?
thanks
pb
Dear Paul, installation instructions in https://sourceforge.net/p/membplugin/wiki/Installation/ have been tested on linux. Please, read carefully and follow those instructions. Then, if you are still experiencing problems don't hesitiate to contact us.
Thank you for the prompt response. I've tried to be very careful about the installation , and installation for linux seems to be the same as that for OS X and Win which work as described- the demos run nicely. Barring some quirk of Linux Mint ( I've got VMD, and Schrodinger working on the same machine ) then I am missing something obvious. It's not for lack of trying - two different Lixux machines behave similarly .
In the meantime is there a command line workaround ?
thanks
Paul
I did try the temporary run method which also failed.
Could you please paste the output of the VMD while opening in a terminal?
What is the output of "puts $VMDDIR" in a TK console?
pb@MSI ~ $ vmd
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a9 (October 19, 2017)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd@ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 15GB (96%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: GeForce GTX 970/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU...
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
vmd > busce004@umn.edu
puts $/home/pb/Desktop/vmd-1.9.3 simply echos
/home/pb/Desktop/vmd-1.9.3
I noticed that MEMB does not recognize the CUDA. But it is installed: nvcc - V does gives the version -9 , and Schrodinger/Desmond sees the GPU as well
With the information that you provided, it is very likely that you have two VMD installs in your computer:
one in /usr/local/lib/vmd/ with 1.9.4a9 VMD version and another one in /home/pb/Desktop/vmd-1.9.3.
Please, check that you are installing the pluging in the same VMD that you run afterwards and modify your PATH variable in .bashrc accordingly for convenience.
Furthermore, installation has not been tested on VMD 1.9.4a9, and MEMBPLUGIN does not use CUDA, so CUDA errors are probably not related with your issue.
Last edit: Ismael Rodriguez Espigares 2017-11-30
What you say is correct, there were two versions. But MEMB did not appear with either v3 or v4 of VMD.
In any event, is there perhaps an alternate command line method of accessing the plugin ?
thanks
Paul
OK.
Please, run again VMD (preferably version 1.9.3) in a terminal and open a TK console (Extensions --> TK Console) . Then, run the following commands in the TK Console and paste here any output printed in the TK console or in the linux terminal after running those commands. Paste also the commands with the actual paths that you used:
puts $env(VMDDIR); # this 'VMDDIR' is literal, do not replace
lappend auto_path /path/to/membplugin-release-1.x/membplugin1.x; # is a directory
source /path/to/membplugin-release-1.x/loadmembplugin.tcl; # is a file
Replace /path/to/membplugin-release-1.x/ with the path to the folder extracted from the release .zip file ("membplugin-release-1.x", membplugin-release-1.1 for membplugin-release-1.1-RC2.zip) and the "x" in membplugin1.x by the current MEMBPLUGIN minor version ("membplugin1.1" for membplugin-release-1.1-RC2.zip). The paths that you write must exist.
lappend auto_path command is crucial to make the plugin working, but we cannot know if it is working correctly until the package is loaded. So, you can try this command:
package require membplugin
to load a minimal package to have at least command-line access (no gui). If this command gives an error in the TK console or in the terminal copy and paste it in the forum.
Run the following commands for more info:
membranescd
lipidarea
interdigitation
lipidtilt
membranethickness
Last edit: Ismael Rodriguez Espigares 2017-11-30
Below is the output from the first commands you suggested. IS this what is anticipated ?
Yes, that is the expected output. The only thing is that it is highly recommended to add only absolute paths (begining with backslash "/") when using "lappend auto_path" command as changing the working directory could make the packages stop working.