VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri May 11 2007 - 07:21:43 CDT

On Fri, 11 May 2007, Francesco Pietra wrote:

francesco,

perhaps it would be better, if you describe in more
detail what you actually intend to do. the usual way
most people operate is to generate the trajectory
somewhere and then transfer the file to a desktop
and visualize/analyze it from the desktop. i don't
quite get, what you mean with 'remote control'.

FP> Axel:
FP> Thanks. Although I'll follow your suggestion to run
FP> tutorials, I find difficult to get rid of my (bad)
FP> mood. That is, first of all I want to have VMD
FP> installed on the x-Gnome-iceweasel-i386 being able to
FP> talk with NAMD installed on the amd64 machine (where
FP> no X system). (Neither one is installed at the moment:
FP> VMD binary version with IMD support, as another kind
FP> guy has suggested?).

please check out the IMD tutorial at:
http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/
to see what is meant by IMD. i'm not sure whether
we are all on the same page here. NAMD is essentially
a text mode program and is executed via (batch) scripts.
IMD is a very special application for very special
problems.

cheers,
   axel.

FP>
FP> I have the VMD 1.8.6 Linux release notes and User's
FP> Guide, though I am unable to find a section describing
FP> how to get remote way of operating. The browser
FP> installed on i386 (iceweasel = Debian version of
FP> firefox) does allow remote control (unlike the
FP> browsers of both KDE and GNOME). I have already set up
FP> successfully such way of remote operating with other
FP> similar systems for MD and the connection between the
FP> two machines was the first thing that I put in order.
FP>
FP> Thanks
FP> francesco
FP>
FP> --- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
FP> wrote:
FP>
FP> > On Wed, 9 May 2007, Francesco Pietra wrote:
FP> >
FP> >
FP> > francesco,
FP> >
FP> > you do _not_ need VMD to run NAMD and vice versa.
FP> > so you can install each of them separately on
FP> > different
FP> > machines in different versions even.
FP> >
FP> > in (unlikely) case you want to do interactive MD
FP> > right away, please check out the corresponding
FP> > tutorials on the NAMD and VMD homepages.
FP> >
FP> > generally, i strongly recommend working through
FP> > a couple of the tutorials before trying something
FP> > serious.
FP> >
FP> > for many cases, it will be sufficient to use the
FP> > precompiled binaries. please make sure that you
FP> > read the release notes for your platform.
FP> >
FP> > ciao,
FP> > axel.
FP> >
FP> >
FP> > FP> I have noticed on the VMD manual a partial
FP> > answer to
FP> > FP> my question below. The partial answer is:
FP> > FP>
FP> > FP> Interactive molecular dynamics simulations VMD
FP> > can be
FP> > FP> used as a graphical front-end to a live
FP> > molecular
FP> > FP> dynamics program running on a remote
FP> > supercomputer or
FP> > FP> high-performance workstation. VMD can
FP> > interactively
FP> > FP> apply and visualize forces in an MD simulation
FP> > as it
FP> > FP> runs.
FP> > FP>
FP> > FP> Is anyone so kind to direct me where to get
FP> > FP> instruction for the connection of VMD to a
FP> > remote
FP> > FP> machine? As I said I already have a reliable ssh
FP> > FP> connection for Linux Debian.
FP> > FP>
FP> > FP> Thanks
FP> > FP> francesco pietra
FP> > FP>
FP> > FP>
FP> > FP>
FP> > FP>
FP> > FP> --- Francesco Pietra <chiendarret_at_yahoo.com>
FP> > wrote:
FP> > FP>
FP> > FP> > Date: Tue, 8 May 2007 23:24:48 -0700 (PDT)
FP> > FP> > From: Francesco Pietra <chiendarret_at_yahoo.com>
FP> > FP> > Subject: vmd first installation
FP> > FP> > To: vmd-l_at_ks.uiuc.edu
FP> > FP> >
FP> > FP> > As a newcomer, interested in vmd for namd,
FP> > before
FP> > FP> > downloading both programs I would like to get
FP> > a
FP> > FP> > piece
FP> > FP> > of information that I was unable (my fault) to
FP> > get
FP> > FP> > from the web pages.
FP> > FP> >
FP> > FP> > I would like to avoid installing vmd on the
FP> > FP> > dual-opteron(s) machine where namd code (and
FP> > other
FP> > FP> > codes, in particular a qm code) are run on
FP> > Debian
FP> > FP> > Linux amd64. Such machine has no graphics
FP> > installed.
FP> > FP> >
FP> > FP> > I would like to install vmd on a ssh-linked
FP> > 32-bit
FP> > FP> > Debian i386 machine, where X and GNOME are
FP> > FP> > installed.
FP> > FP> > This is the way I use other graphical
FP> > interfaces,
FP> > FP> > just
FP> > FP> > to avoid to slow down the 64-bit machine.
FP> > That
FP> > FP> > means
FP> > FP> > that I am able to slogin from either machine
FP> > to the
FP> > FP> > other one (public keys), and to use any
FP> > standard ssh
FP> > FP> > command, although I can't act as server
FP> > because I
FP> > FP> > have
FP> > FP> > a dynamic dhcp, and use static dhcp as
FP> > internally
FP> > FP> > provided by the router.
FP> > FP> >
FP> > FP> > Also, I am just an organic chemist, absolutely
FP> > not
FP> > FP> > an
FP> > FP> > expert in informatics.
FP> > FP> >
FP> > FP> > Thanks for help
FP> > FP> >
FP> > FP> > francesco pietra
FP> > FP> >
FP> > FP> >
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FP> >
FP> > --
FP> >
FP> =======================================================================
FP> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
FP> > http://www.cmm.upenn.edu
FP> > Center for Molecular Modeling -- University
FP> > of Pennsylvania
FP> > Department of Chemistry, 231 S.34th Street,
FP> > Philadelphia, PA 19104-6323
FP> > tel: 1-215-898-1582, fax: 1-215-573-6233,
FP> > office-tel: 1-215-898-5425
FP> >
FP> =======================================================================
FP> > If you make something idiot-proof, the universe
FP> > creates a better idiot.
FP> >
FP> >
FP>
FP>
FP>
FP>
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.