VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Jan 12 2015 - 11:40:34 CST

One thing I would add is that rlwrap doesn't work with the csh launch
script, but it works just fine with the bash one. I think its due to how
debian passes its environment variables to other shells.
-Josh

On 01/12/2015 10:37 AM, John Stone wrote:
> 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/