From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri May 11 2007 - 11:05:08 CDT

John:
Thanks and please see below my apologies.

--- John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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.

I apologize for having been generic, though your
guidelines above fully answer my request. I am
carrying out a long vibrational analysis for a large
molecules at high basis set on amd64; as soon as
ready, I'll try to install NAMD/VMD.

francesco
>
> 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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> >
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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
>

 
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