VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 30 2007 - 16:34:37 CDT

Hi,
  I've got a build of VMD installed, and the IU staff are in the process
of adding it to the BigRed software environment system they use.
For the moment, you should be able to run VMD with:
  /N/soft/linux-sles9-ppc64/vmd-1.8.6/bin/vmd

This is a special text-mode-only build with no graphics support.
Let me know if you have any trouble using it for your purposes.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 30, 2007 at 02:06:11PM -0500, John Stone wrote:
> Hi,
> It appears the IU staff have now resolved my login issues on BigRed,
> so I will begin building VMD forthwith!
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, May 30, 2007 at 02:50:21PM -0400, Yinglong Miao wrote:
> > John,
> >
> > I talked to my advisor Peter Ortoleva about the situation of building
> > VMD on BigRed. He called you about it and asked me to send you
> > information about what I want from VMD. Basically the functions
> > handling dcd, pdb files and atom selections are what I need for my
> > simulations.
> >
> > Thanks,
> > Long
> >
> > Quoting John Stone <johns_at_ks.uiuc.edu>:
> >
> > >
> > >Hi,
> > > I've been planning on doing a VMD build for BigRed, but had
> > >some difficulty getting my account setup over there, so it lagged
> > >by several weeks as I got busy with other things. In principle
> > >building VMD for BigRed should be no problem, it mainly involves
> > >doing a non-GUI build, which is not hard. I can walk you through the
> > >process of building VMD, or if you can wait a bit, I should be able
> > >to get my BigRed account sorted out and finally do a build, as
> > >I know there are quite a few people that want to run VMD on
> > >BigRed for remote analysis etc. If you want to take a crack
> > >at it, should be able to help you out if you're in a hurry.
> > >
> > >Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >
> > >On Fri, May 25, 2007 at 05:59:11PM -0400, Yinglong Miao wrote:
> > >>Dear all,
> > >>
> > >>I have been haunted by a problem with installing VMD on a LINUX
> > >>cluster, BigRed, at IU. BigRed consists of 512 IBM JS21 Blades, each
> > >>with two dual-core PowerPC processors and runs SuSE Linux Enterprise
> > >>Server operating system (see
> > >>http://uits.iu.edu/scripts/ose.cgi?aueo.def.help).
> > >>
> > >>I was told that BigRed doesn't support OpenGL and even has issues with
> > >>X. And VMD cannot be installed with GUI. But I want to use VMD for
> > >>numerical analyses of NAMD simulation outputs by making use of VMD
> > >>plugins. Also for my current NAMD simulations, I need to call TCL
> > >>scripts which need to be interpreted by VMD with its plugins (some
> > >>basic functions handling dcd, pdb files, atom selection , etc.). So I
> > >>want to ask is there a way to have VMD installed as a TCL interpreter
> > >>executed with "vmd -dispdev text -e myscript.tcl" without worrying
> > >>about the graphics support?
> > >>
> > >>There were some discussions in previous posts about "vmd can't start up
> > >>after being installed in linux" (lanhua Tue Apr 17 2007), but I didn't
> > >>find my answers there. Do you have any more ideas?
> > >>
> > >>Best regards,
> > >>Long
> > >>
> > >>
> > >>--
> > >>Yinglong Miao
> > >>Ph.D. Candidate
> > >>Center for Cell and Virus Theory
> > >>Department of Chemistry, C203A
> > >>Indiana University
> > >>800 E. Kirkwood Ave.
> > >>Bloomington, Indiana 47405
> > >>1-812-856-0981 (office)
> > >>1-812-857-6205 (home)
> > >>http://ylmiao.dict.cn/mypage/
> > >
> > >--
> > >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
> > >
> >
> >
> >
> > --
> > Yinglong Miao
> > Ph.D. Candidate
> > Center for Cell and Virus Theory
> > Department of Chemistry, C203A
> > Indiana University
> > 800 E. Kirkwood Ave.
> > Bloomington, Indiana 47405
> > 1-812-856-0981 (office)
> > 1-812-857-6205 (home)
> > http://ylmiao.dict.cn/mypage/
>
> --
> 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 

-- 
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