VMD-L Mailing List

From: Arnab Mukherjee (arnab_at_chimie.ens.fr)
Date: Wed Jul 04 2007 - 16:11:36 CDT

Hi everybody,
I have seen a similar post but not exactly this one which I am facing.
I have redhat enterprize linux v5. I installed vmd from AMD64 binary. When I
am typing vmd, the whole screen becomes black and then I am logged out.

Actually I was fine initially and vmd was working fine. Then I updated many
libraries etc. installed lesstif etc for xmgrace and corresponding libraries
which are required by grace. But after all that now I face the problem with
vmd.

Following the previous post on "vmd crashes on startup", I give the
informations below:
uname -a shows the output below
Linux squire5.colorado.edu 2.6.18-8.1.6.el5 #1 SMP Fri Jun 1 18:52:13 EDT
2007 x86_64 x86_64 x86_64 GNU/Linux

I have nvidia graphics card
vmd -debug | run |where shows "No stack" output

Your comments/suggestions will be very much appreciated.

Thanks
Arnab

On 7/4/07, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> On Tue, 3 Jul 2007, Zhimin Xiong wrote:
>
> hi!
>
> ZX> Hi, all, I am asking for your help when viewing molecular dynamics
> ZX> trajectory. For example, I want to display the polymer chain
> configuration
> ZX> from MD trajectory file, however, given the psf file that contains the
> ZX> connectivity of the monomer along the chain, some of the bonds cross
> over
> ZX> the box boundary, so the bonds displayed is not true. One way I
> thought to
> ZX> solve it is to view a specific frame of the trajectory file and give
> the
> ZX> connectivity psf file for this frame that don't connect the crossing
> bonds,
> ZX> but it is not convenient to view a lot of frames sequentially. Any
> ZX> suggestion is appreciated!
>
> right now i can think of two options that might help you.
>
> 1) you can try the DynamicBonds representation. this works best, if
> your bond lengths are rather homogeneous.
>
> 2) you can re-apply PBC in a way that only whole molecules are
> subject to box crossings. the PBCtools plugin in VMD should
> be able to help you with that, but also several MD packages
> have tools to handle this or settings to create corresponding
> trajectories.
>
> cheers,
> axel.
>
> --
> =======================================================================
> 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.
>
> 

-- 
Dr. Arnab Mukherjee
Post doctorate
Theoretical Chemistry
Departement de Chimie
Ecole Normale Superieure
Rue d'Ulm, Paris-75005
France