VMD-L Mailing List

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Mon May 28 2007 - 22:54:54 CDT

John,

I'd like to take a try on it if you can send me some instructions.

Thanks,
Long

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Monday, May 28, 2007 3:44 PM
To: Yinglong Miao
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: problem with installing VMD on a LINUX cluster

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