VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 13 2015 - 01:16:34 CST

Also, some shell scripts do use as the 1st line:

#/bin/sh

but are actually written in bash, so should use:

#/bin/bash

I remember that ubuntus /bin/sh is a link against /bin/dash, which wouldn't
correctly execute scripts written in bash. So maybe this could also be the
problem. It's usually no problem to relink /bin/sh against /bin/bash to
prevent such problems:

ls /bin/sh

if it is a symlink:

rm /bin/sh
ln -s /bin/bash /bin/sh

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Josh Vermaas
> Gesendet: Montag, 12. Januar 2015 18:41
> An: John Stone; Francesco Pietra; VMD Mailing List
> Betreff: Re: Fwd: vmd-l: VMD 1.9.2 released!
>
> 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=KLEI
> 2014-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=KLEI201
> 4-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/