From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 12 2015 - 10:37:35 CST

Francesco,
  I would suggest that you disable 'rlwrap' in the VMD startup script if
it is preventing you from running VMD on Ubuntu. I'm not sure what would
be causing problems there, but the use of 'rlwrap' by VMD is really just a
convenience to get GNU readline input support ex post facto without making
significant changes to VMD itself. You can use VMD just fine without it
if you disable it. It would be nice to know what is going wrong with
rlwrap on Ubuntu, but it probably wouldn't be too hard to adjust the
VMD startup script to skip it if rlwrap is badly broken on Ubuntu.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 07, 2015 at 07:43:45AM +0100, Francesco Pietra wrote:
> Hi John:
> 2015. Should really rlwrap be disabled with 1.9.2 by Debian users or you
> can find a turnaround?
> thanks
> francesco
> ---------- Forwarded message ----------
> From: Francesco Pietra <[1]chiendarret_at_gmail.com>
> Date: Wed, Dec 31, 2014 at 6:39 PM
> Subject: Re: vmd-l: VMD 1.9.2 released!
> To: John Stone <[2]johns_at_ks.uiuc.edu>, Francesco Pietra
> <[3]chiendarret_at_gmail.com>, VMD Mailing List <[4]vmd-l_at_ks.uiuc.edu>
>
> John:
> I don't want to bother you further at the end of the year. We can review
> the matter next year.
> Anyway, I have reinstalled 1.9.1, removing rlwrap. Reinstalled the latter,
> just to answer your questions:
>
> francesco_at_tya64:~$ which rlwrap
> /usr/bin/rlwrap
>
> francesco_at_tya64:~$ rlwrap
> Usage: rlwrap [options] command ...
>
> Options:
> A -a[password:]A A A A A A A A A A A A A --always-readline[=password:]
> A -AA A A A A A A A A A A A A A A A A A A A A A A A --ansi-colour-aware
> A -bA <chars>A A A A A A A A A A A A A A A --break-chars=<chars>
> A -cA A A A A A A A A A A A A A A A A A A A A A A A --complete-filenames
> A -CA <name|N>A A A A A A A A A A A A A A --command-name=<name|N>
> A -DA <0|1|2>A A A A A A A A A A A A A A A --history-no-dupes=<0|1|2>
> A -fA <completion list>A A A A A --file=<completion list>
> A -gA <regexp>A A A A A A A A A A A A A A --forget-matching=<regexp>
> A -hA A A A A A A A A A A A A A A A A A A A A A A A --help
> A -HA <file>A A A A A A A A A A A A A A A A --history-filename=<file>
> A -iA A A A A A A A A A A A A A A A A A A A A A A A --case-insensitive
> A -IA A A A A A A A A A A A A A A A A A A A A A A A
> --pass-sigint-as-sigterm
> A -lA <file>A A A A A A A A A A A A A A A A --logfile=<file>
> A -nA A A A A A A A A A A A A A A A A A A A A A A A --no-warnings
> A -NA A A A A A A A A A A A A A A A A A A A A A A A --no-children
> A -oA A A A A A A A A A A A A A A A A A A A A A A A --one-shot
> A -OA <regexp>A A A A A A A A A A A A A A --only-cook=<regexp>
> A -p[colour]A A A A A A A A A A A A A A A A --prompt-colour[=colour]
> A -PA <input>A A A A A A A A A A A A A A A --pre-given=<input>
> A -qA <chars>A A A A A A A A A A A A A A A --quote-characters=<chars>
> A -m[newline substitute]A A A A --multi-line[=newline substitute]
> A -rA A A A A A A A A A A A A A A A A A A A A A A A --remember
> A -RA A A A A A A A A A A A A A A A A A A A A A A A --renice
> A -vA A A A A A A A A A A A A A A A A A A A A A A A --version
> A -sA <N>A A A A A A A A A A A A A A A A A A A --histsize=<N>
> (negative: readonly)
> A -SA <prompt>A A A A A A A A A A A A A A --substitute-prompt=<prompt>
> A -tA <name>A A A A A A A A A A A A A A A A --set-term-name=<name>
> A -wA <N>A A A A A A A A A A A A A A A A A A A --wait-before-prompt=<N>
> (msec, <0A : patient mode)
> A -zA <filter command>A A A A A A --filter=<filter command>
>
> Have a nice slide into 2015
>
> francesco
> On Wed, Dec 31, 2014 at 5:10 PM, John Stone <[5]johns_at_ks.uiuc.edu> wrote:
>
> Francesco,
> A Although you have rlwrap on your system, is /usr/bin in your path?
> What happens if you run this command:
> A which rlwrap
>
> If you run rlwrap by hand, do you get any error?
>
> You can of course edit the VMD startup script and simply
> disable the use of rlwrap, as it is only used to gain some of the
> benefits of command line editing and the like.
>
> Cheers,
> A John Stone
> A [6]vmd_at_ks.uiuc.edu
> On Wed, Dec 31, 2014 at 04:17:55PM +0100, Francesco Pietra wrote:
> >A A I unistalled vmd 1.9.1 from my old amd dual opteron box running
> gnu linux
> >A A debian amd64 wheezy. No CUDA.
> >
> >A A I installed vmd 1.9.2, cheking first
> >
> >A A :~$ which rlwrap
> >A A /usr/bin/rlwrap
> >
> >A A However
> >
> >A A ~$ vmd
> >A A rlwrap: No match.
> >
> >A A I have found a lot of chats on internet about vmd/rlwrap for
> ubuntu OS.
> >A A You know that ubuntu was made to be largely incompatible with
> debian,
> >A A unlike others, like mint for example, that are fully compatible
> Could the
> >A A developers please indicate how to have vmd 1.9.2 running with
> debian
> >A A amd64? For the time being I am going to reinstall 1.9.1 as my
> duties with
> >A A students leave me little time to solve idiosyncrasies of
> software.
> >
> >A A Thanks a lot
> >
> >A A francesco pietra
> >
> >A A On Tue, Dec 30, 2014 at 8:47 PM, John Stone
> <[1][7]johns_at_ks.uiuc.edu> wrote:
> >
> >A A A Dear VMD-L,
> >A A A AA I've just posted the final VMD 1.9.2 release builds on the
> >A A A web site.AA The new version includes many new features, and a
> variety
> >A A A new plugins and tools contributed by many members of the VMD
> user
> >A A A community.
> >
> >A A A A brief summary of new features in VMD is included below:
> >
> >A A A What's new in VMD 1.9.2?
> >A A A ------------------------
> >A A A AA New Features and Performance Improvements
> >A A A AA AA o Fast GPU-accelerated quality-of-fit cross
> correlation enables
> >A A A AA AA AA analysis of results from molecular dynamics
> flexible fitting
> >A A A (MDFF)
> >A A A AA AA AA and other hybrid structure determination methods:
> >A A A AA AA AA [2][8]http://dx.doi.org/10.1039/C4FD00005F
> >A A A AA AA o New built-in TachyonL-OptiX GPU-accelerated ray
> tracing engine
> >A A A AA AA AA speeds up high quality image and movie renderings,
> particularly
> >A A A AA AA AA for scenes using ambient occlusion lighting and
> shadows:
> >A A A AA AA AA [3][9]http://dx.doi.org/10.1145/2535571.2535595
> >A A A AA AA o VMD now includes a built-in implementation of the
> collective
> >A A A variables
> >A A A AA AA AA feature also implemented in NAMD, enabling easier
> preparation
> >A A A AA AA AA and analysis of NAMD simulations using collective
> variables:
> >A A A AA AA AA
> [4][10]http://dx.doi.org/10.1080/00268976.2013.813594
> >A A A AA AA o Built-in support for parallel analysis and
> visualization using
> >A A A AA AA AA MPI, with new VMD "parallel" commands:
> >A A A AA AA AA [5][11]http://dx.doi.org/10.1109/XSW.2013.10
> >A A A AA AA o Added initial support for large scale parallel
> scripting with
> >A A A Swift/T:
> >A A A AA AA AA [6][12]http://www.ks.uiuc.edu/Research/swift/
> >A A A AA AA o VMD supports off-screen OpenGL rendering, enabling
> large
> >A A A AA AA AA scale parallel visualization runs on "headless"
> GPU clusters
> >A A A and
> >A A A AA AA AA petascale computers, using a new "-dispdev
> openglpbuffer" flag:
> >A A A AA AA A
> >A A A
> [7][13]http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=KLEI2014-JS
> >A A A AA AA o An improved "QuickSurf" molecular surface
> representation allows
> >A A A AA AA AA molecular dynamics trajectories to be animated for
> selections
> >A A A of
> >A A A AA AA AA 10,000 to over 1,000,000 atoms depending on the
> speed of the
> >A A A AA AA AA host machine.AA Fast multi-core and
> GPU-accelerated
> >A A A implementations
> >A A A AA AA AA of the QuickSurf representation enable
> faster/smoother
> >A A A AA AA AA trajectory playback for moderate system sizes, and
> interactive
> >A A A AA AA AA surface calculation for systems containing up to
> 100 million
> >A A A atoms
> >A A A AA AA AA on machines with sufficient host and GPU memory
> capacity:
> >A A A AA AA A
> >A A A
> [8][14]http://dx.doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071
> >A A A AA AA AA [9][15]http://dx.doi.org/10.1145/2535571.2535595
> >A A A AA AA o The improved QuickSurf implementation now supports
> visualization
> >A A A AA AA AA of coarse-grained and cellular scale models:
> >A A A AA AA AA [10][16]http://dx.doi.org/10.1002/jcc.23130
> >A A A AA AA AA
> [11][17]http://dx.doi.org/10.1016/j.parco.2014.03.009
> >
> >A A A AA Other updates and improvements
> >A A A AA AA o Added initial support for ARM processors and the
> Android OS
> >A A A AA AA o Added support for compilation of VMD with Tcl 8.6.x
> >
> >A A A AA New and improved plugins and extensions
> >A A A AA AA o Bendix: calculates and visualizes both dynamic and
> static
> >A A A AA AA AA helix geometry, and abstracts helices without
> sacrificing
> >A A A conformation:
> >A A A AA AA AA [12][18]http://sbcb.bioch.ox.ac.uk/Bendix/
> >A A A AA AA o FFTK: The Force Field Toolkit (FFTK) plugin is a set
> of tools
> >A A A AA AA AA that aid users in the development of
> CHARMM-compatible force
> >A A A AA AA AA field parameters, including: charges, bonds,
> angles, and
> >A A A dihedrals
> >A A A AA AA AA
> [13][19]http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> >A A A AA AA o MDFF: added option in mdff setup to use implicit
> solvent
> >A A A AA AA o NetworkView: a plugin for the study of allostery and
> signalling
> >A A A AA AA AA through network models, allowing networks can be
> loaded and
> >A A A mapped onto
> >A A A AA AA AA molecular structures loaded in VMD
> >A A A AA AA o NMWiz: A normal mode analysis plugin
> >A A A AA AA o psfgen: Add non-plugin NAMD binary file writing
> command
> >A A A "writenamdbin".
> >A A A AA AA AA Properly handle insertion codes by appending the
> code to the
> >A A A AA AA AA resid string as in "48A".AA Read and write
> insertion code in
> >A A A resid
> >A A A AA AA AA field of psf file.AA Add "readpsf file.psf pdb
> file.pdb" to
> >A A A AA AA AA read insertion code from pdb file.AA Add
> "regenerate resids" to
> >A A A AA AA AA remove insertion codes with minimal residue
> renumbering.
> >A A A AA AA AA Leave atoms in reasonable order when applying
> patches.
> >A A A AA AA AA Do not generate O-H-H angles (assume these are
> water
> >A A A molecules).
> >A A A AA AA AA Free old memory when regenerating angles or
> dihedrals for
> >A A A AA AA AA entire structure.AA Handle masses as large as
> 99999.
> >A A A AA AA AA Use 6-wide atom type when writing CHARMM EXT
> format X-PLOR psf
> >A A A file.
> >A A A AA AA AA Use field width of 10 when reading CHARMM EXT
> >A A A AA AA AA angles/dihedrals/impropers/cmaps.
> >A A A AA AA o Remote: A plugin for managing VMD remote control
> connections
> >A A A AA AA AA from mobile phones and wireless tablet devices
> >A A A AA AA o Timeline: improved graphical interface with better
> zooming, and
> >A A A AA AA AA improved display of very long timescale
> trajectories
> >A A A AA AA o topotools: New topogromacs features,
> >A A A AA AA AA allow support replication of non-orthogonal cells,
> >A A A AA AA AA handle low-dimensional system box dimensions
> consistent with
> >A A A LAMMPS,
> >A A A AA AA AA fix bug in writing non-orthogonal boxes reported
> by Sandeep
> >A A A Kumar Reddy,
> >A A A AA AA AA add support for new Coeff section in LAMMPS data
> files,
> >A A A AA AA AA add support for writing LAMMPS data files with
> triclinic cells.
> >A A A AA AA o Modified TkCon to prevent it from sourcing command
> line args
> >A A A AA AA AA as script files at startup.
> >
> >A A A AA New and improved file import and export
> >A A A AA AA o cubeplugin: Make the parser for the cubefile header
> more
> >A A A resilient
> >A A A AA AA AA when new fields are added like in g09 rev d.01.
> >A A A AA AA o dcdplugin: Changed the dcdplugin reader code to
> avoid using
> >A A A readv()
> >A A A AA AA AA to prevent problems when reading 240M-atom
> trajectories on some
> >A A A AA AA AA versions of Linux.
> >A A A AA AA o dlpolyplugin: Fixed a typo in the PBC unit cell
> basis vector
> >A A A AA AA AA orthogonality check.
> >A A A AA AA o gamessplugin: Fixed reading of minimization steps
> for recent
> >A A A AA AA AA builds of Firefly 8
> >A A A AA AA o gromacsplugin: Updates to gromacsplugin adding .gro
> write
> >A A A support,
> >A A A AA AA AA contributed by Magnus Lundborg.AA Changed .gro
> parsing code to
> >A A A use
> >A A A AA AA AA fixed field widths to address problems with files
> that had no
> >A A A AA AA AA spaces between the coordinate fields.
> >A A A AA AA o jslugin: Changed the jsplugin reader code to avoid
> using readv()
> >A A A AA AA AA to prevent problems when reading 240M-atom
> trajectories on some
> >A A A AA AA AA versions of Linux.
> >A A A AA AA o lammpsplugin: Support LAMMPS native trajectories
> with variable
> >A A A AA AA AA number of atoms through provisioning constant
> storage via an
> >A A A AA AA AA environment variable LAMMPSMAXATOM.
> >A A A AA AA AA Fixed bug in handling triclinic cells with
> negative tilt
> >A A A factors.
> >A A A AA AA o maeffplugin: Fixed uninitialized optflags state in
> maeffplugin,
> >A A A so
> >A A A AA AA AA that compilations that don't define
> DESRES_CTNUMBER will behave
> >A A A correctly.
> >A A A AA AA o moldenplugin: Fixed various limitations that had
> previously
> >A A A AA AA AA caused problems for Terachem users. Use
> case-insensitive string
> >A A A AA AA AA comparisons when reading shell types from Molden
> files.
> >A A A AA AA o molemeshplugin: Added Brian Bennion's plugin for
> reading mesh
> >A A A files
> >A A A AA AA AA produced by MOLE 2.0.
> >A A A AA AA o offplugin: Fixed internal initialization bug
> >A A A AA AA o psfplugin: Handle various
> bond/angle/dihedral/improper
> >A A A AA AA AA misformattings for 10M-100M-atom structures.
> >A A A AA AA AA Made the PSF plugin allow NAMD-tagged PSF files to
> use a
> >A A A AA AA AA space delimited bond record format since NAMD
> accepts that
> >A A A variation.
> >A A A AA AA o rst7plugin: Added support for reading and writing
> box
> >A A A AA AA AA and velocity information.
> >A A A AA AA o tngplugin: Added support for the new Gromacs TNG
> plugin
> >A A A AA AA o vtfplugin: Allow compilation of VTF plugin without
> Tcl,
> >A A A AA AA AA updated to latest version by Olaf Lenz
> >A A A AA AA o xsfplugin: Fixed a problem with the interpretation
> of the cell
> >A A A AA AA AA vectors in cases that must be rotated.
> >
> >A A A AA User documentation updates
> >A A A AA AA o Minor improvements and corrections to the VMD User's
> Guide,
> >A A A AA AA AA added documentation for new commands, graphical
> >A A A representations,
> >A A A AA AA AA and environment variables.
> >A A A AA AA o parsefep: Updated ParseFEP docs with latest files
> from Chris
> >A A A Chipot.
> >A A A AA AA o vdna: Updated Tom Bishop's contact info in the docs
> >
> >A A A AA Bug fixes and small improvements
> >A A A AA AA o NetworkView: small GUI improvements and fixes
> >A A A AA AA o fftk: fixes to GenZMatrix to allow for more general
> ACC/DON
> >A A A assignments
> >A A A AA AA o Fixed a potential crash in the x86 SSE-accelerated
> version of
> >A A A the
> >A A A AA AA AA wavefunction calculation for the Orbital
> representation
> >A A A AA AA o Fixed an Interactive MD force cancellation bug that
> occured most
> >A A A AA AA AA frequently when using Mouse-based control and
> multi-atom
> >A A A targets
> >A A A AA AA o Fixed an old bug with 2-atom and 3-atom alignments
> >A A A AA AA o Fixed a bug prevented clean compilations without
> Tcl,
> >A A A AA AA AA needed for early Android testing.
> >A A A AA AA o Updated the VMD copy of WKFThreads from the latest
> version of
> >A A A Tachyon.
> >
> >A A A Cheers,
> >A A A AA John Stone
> >A A A AA [14][20]vmd_at_ks.uiuc.edu
> >A A A --
> >A A A NIH Center for Macromolecular Modeling and Bioinformatics
> >A A A Beckman Institute for Advanced Science and Technology
> >A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >A A A [15][21]http://www.ks.uiuc.edu/~johns/AA AA AA AA AA A
> Phone:
> >A A A [16]217-244-3349
> >A A A [17][22]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> >A A Visible links
> >A A 1. mailto:[23]johns_at_ks.uiuc.edu
> >A A 2. [24]http://dx.doi.org/10.1039/C4FD00005F
> >A A 3. [25]http://dx.doi.org/10.1145/2535571.2535595
> >A A 4. [26]http://dx.doi.org/10.1080/00268976.2013.813594
> >A A 5. [27]http://dx.doi.org/10.1109/XSW.2013.10
> >A A 6. [28]http://www.ks.uiuc.edu/Research/swift/
> >A A 7.
> [29]http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=KLEI2014-JS
> >A A 8.
> [30]http://dx.doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071
> >A A 9. [31]http://dx.doi.org/10.1145/2535571.2535595
> >A A 10. [32]http://dx.doi.org/10.1002/jcc.23130
> >A A 11. [33]http://dx.doi.org/10.1016/j.parco.2014.03.009
> >A A 12. [34]http://sbcb.bioch.ox.ac.uk/Bendix/
> >A A 13. [35]http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> >A A 14. mailto:[36]vmd_at_ks.uiuc.edu
> >A A 15. [37]http://www.ks.uiuc.edu/~johns/
> >A A 16. tel:[38]217-244-3349
> >A A 17. [39]http://www.ks.uiuc.edu/Research/vmd/
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [40]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> [41]217-244-3349
> [42]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:chiendarret_at_gmail.com
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:chiendarret_at_gmail.com
> 4. mailto:vmd-l_at_ks.uiuc.edu
> 5. mailto:johns_at_ks.uiuc.edu
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. mailto:johns_at_ks.uiuc.edu
> 8. http://dx.doi.org/10.1039/C4FD00005F
> 9. http://dx.doi.org/10.1145/2535571.2535595
> 10. http://dx.doi.org/10.1080/00268976.2013.813594
> 11. http://dx.doi.org/10.1109/XSW.2013.10
> 12. http://www.ks.uiuc.edu/Research/swift/
> 13. http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=KLEI2014-JS
> 14. http://dx.doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071
> 15. http://dx.doi.org/10.1145/2535571.2535595
> 16. http://dx.doi.org/10.1002/jcc.23130
> 17. http://dx.doi.org/10.1016/j.parco.2014.03.009
> 18. http://sbcb.bioch.ox.ac.uk/Bendix/
> 19. http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> 20. mailto:vmd_at_ks.uiuc.edu
> 21. http://www.ks.uiuc.edu/~johns/A
> 22. http://www.ks.uiuc.edu/Research/vmd/
> 23. mailto:johns_at_ks.uiuc.edu
> 24. http://dx.doi.org/10.1039/C4FD00005F
> 25. http://dx.doi.org/10.1145/2535571.2535595
> 26. http://dx.doi.org/10.1080/00268976.2013.813594
> 27. http://dx.doi.org/10.1109/XSW.2013.10
> 28. http://www.ks.uiuc.edu/Research/swift/
> 29. http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=KLEI2014-JS
> 30. http://dx.doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071
> 31. http://dx.doi.org/10.1145/2535571.2535595
> 32. http://dx.doi.org/10.1002/jcc.23130
> 33. http://dx.doi.org/10.1016/j.parco.2014.03.009
> 34. http://sbcb.bioch.ox.ac.uk/Bendix/
> 35. http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> 36. mailto:vmd_at_ks.uiuc.edu
> 37. http://www.ks.uiuc.edu/~johns/
> 38. tel:217-244-3349
> 39. http://www.ks.uiuc.edu/Research/vmd/
> 40. http://www.ks.uiuc.edu/~johns/
> 41. tel:217-244-3349
> 42. http://www.ks.uiuc.edu/Research/vmd/

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/