VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri May 11 2007 - 02:50:29 CDT

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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