VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 11 2007 - 10:51:53 CDT

Francesco,
  The configuration you describe (NAMD on your amd64 machine,
communicating with VMD via IMD) should be no problem. You simply
install NAMD on the amd64 machine, and install VMD on whatever
other machine you like. Making them communicate with each other is
simply a matter of loading the same structures in both NAMD and VMD,
enabling IMD in the NAMD config file, and either using text commands
or the Extensions->Simulation->IMD Connect menu item.

There are some IMD-specific tutorials here:
  http://www.ks.uiuc.edu/Research/vmd/imd/

>From your emails, it wasn't clear to me what precisely you need help
with. It's much easier for us to answer specific questions than general
ones, so if you can tell us what specific problems you need help with,
we should be able to help you more effectively.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 11, 2007 at 12:50:29AM -0700, Francesco Pietra wrote:
> Axel:
> Thanks. Although I'll follow your suggestion to run
> tutorials, I find difficult to get rid of my (bad)
> mood. That is, first of all I want to have VMD
> installed on the x-Gnome-iceweasel-i386 being able to
> talk with NAMD installed on the amd64 machine (where
> no X system). (Neither one is installed at the moment:
> VMD binary version with IMD support, as another kind
> guy has suggested?).
>
> I have the VMD 1.8.6 Linux release notes and User's
> Guide, though I am unable to find a section describing
> how to get remote way of operating. The browser
> installed on i386 (iceweasel = Debian version of
> firefox) does allow remote control (unlike the
> browsers of both KDE and GNOME). I have already set up
> successfully such way of remote operating with other
> similar systems for MD and the connection between the
> two machines was the first thing that I put in order.
>
> Thanks
> francesco
>
> --- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> wrote:
>
> > On Wed, 9 May 2007, Francesco Pietra wrote:
> >
> >
> > francesco,
> >
> > you do _not_ need VMD to run NAMD and vice versa.
> > so you can install each of them separately on
> > different
> > machines in different versions even.
> >
> > in (unlikely) case you want to do interactive MD
> > right away, please check out the corresponding
> > tutorials on the NAMD and VMD homepages.
> >
> > generally, i strongly recommend working through
> > a couple of the tutorials before trying something
> > serious.
> >
> > for many cases, it will be sufficient to use the
> > precompiled binaries. please make sure that you
> > read the release notes for your platform.
> >
> > ciao,
> > axel.
> >
> >
> > FP> I have noticed on the VMD manual a partial
> > answer to
> > FP> my question below. The partial answer is:
> > FP>
> > FP> Interactive molecular dynamics simulations VMD
> > can be
> > FP> used as a graphical front-end to a live
> > molecular
> > FP> dynamics program running on a remote
> > supercomputer or
> > FP> high-performance workstation. VMD can
> > interactively
> > FP> apply and visualize forces in an MD simulation
> > as it
> > FP> runs.
> > FP>
> > FP> Is anyone so kind to direct me where to get
> > FP> instruction for the connection of VMD to a
> > remote
> > FP> machine? As I said I already have a reliable ssh
> > FP> connection for Linux Debian.
> > FP>
> > FP> Thanks
> > FP> francesco pietra
> > FP>
> > FP>
> > FP>
> > FP>
> > FP> --- Francesco Pietra <chiendarret_at_yahoo.com>
> > wrote:
> > FP>
> > FP> > Date: Tue, 8 May 2007 23:24:48 -0700 (PDT)
> > FP> > From: Francesco Pietra <chiendarret_at_yahoo.com>
> > FP> > Subject: vmd first installation
> > FP> > To: vmd-l_at_ks.uiuc.edu
> > FP> >
> > FP> > As a newcomer, interested in vmd for namd,
> > before
> > FP> > downloading both programs I would like to get
> > a
> > FP> > piece
> > FP> > of information that I was unable (my fault) to
> > get
> > FP> > from the web pages.
> > FP> >
> > FP> > I would like to avoid installing vmd on the
> > FP> > dual-opteron(s) machine where namd code (and
> > other
> > FP> > codes, in particular a qm code) are run on
> > Debian
> > FP> > Linux amd64. Such machine has no graphics
> > installed.
> > FP> >
> > FP> > I would like to install vmd on a ssh-linked
> > 32-bit
> > FP> > Debian i386 machine, where X and GNOME are
> > FP> > installed.
> > FP> > This is the way I use other graphical
> > interfaces,
> > FP> > just
> > FP> > to avoid to slow down the 64-bit machine.
> > That
> > FP> > means
> > FP> > that I am able to slogin from either machine
> > to the
> > FP> > other one (public keys), and to use any
> > standard ssh
> > FP> > command, although I can't act as server
> > because I
> > FP> > have
> > FP> > a dynamic dhcp, and use static dhcp as
> > internally
> > FP> > provided by the router.
> > FP> >
> > FP> > Also, I am just an organic chemist, absolutely
> > not
> > FP> > an
> > FP> > expert in informatics.
> > FP> >
> > FP> > Thanks for help
> > FP> >
> > FP> > francesco pietra
> > 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.
> >
> >
>
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078