VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 09 2008 - 01:48:46 CDT

Hi,
  Most likely you're using one of the buggy Linux kernels that
has problems with pthreads. Please see the VMD Linux release notes
for more information on this issue and how to update your system to
a non-buggy kernel:
  http://www.ks.uiuc.edu/Research/vmd/current/linuxrelnotes.html

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Tue, Sep 09, 2008 at 11:31:33AM +0530, gaurav nandrajog wrote:
> respected Sir,
> whenever i load my molecule in vmd it suddenly disappears without
> any message. i am using vmd 1.8.6 in red hat linux 4. i tried a lot of
> things but didnt find anything. plz help me out.
>
> On Mon, Sep 8, 2008 at 10:11 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Rabab,
> > How did you get the min/max coordinates that you used in the command
> > you specified below? Those coordinates are clearly quite a ways
> > away from the lone water that you began with. I believe that the sole
> > reason for your problem is that you're specifying min/max coordinates
> > that are offset from your original water. How did you input the min/max
> > coordinates originally?
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Sep 02, 2008 at 08:35:50PM -0700, Rabab Toubar wrote:
> > > hi,
> > >
> > > I was solvating a water molecule with water as a solvent. The command I
> > used was :
> > > package require solvate
> > > solvate water.psf water.pdb -o water_solv -s WT -b 2.4 -minmax {
> > {-4.597000002861 16.4689998627 0.34399995804} {32.6819992065 52.2010002136
> > 30.9549999237}}
> > >
> > > Checking the produced pdb file (water_solv.pdb:
> > > http://www.uploading.com/files/AFLHVFZN/water_solv.pdb.html
> > > I found out that the initial water molecule was outside the solvent box
> > and the minmax coordinates were differnet than the input coordinates.
> > > I was wondering is there a need to "Translate" the initial water molecule
> > before using it in NAMD?
> > >
> > > Thanks
> > > Rabab
> > >
> > > --- On Tue, 9/2/08, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > From: John Stone <johns_at_ks.uiuc.edu>
> > > Subject: Re: vmd-l: solvating a water molecule
> > > To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > > Cc: vmd-l_at_ks.uiuc.edu
> > > Date: Tuesday, September 2, 2008, 5:16 PM
> > >
> > > Hi,
> > > It's not clear what you did that's giving you the behavior
> > > you are describing. Your statements are too vague to interpret.
> > >
> > > In order for anyone to help you, we would need much more
> > > detail about what steps you followed and what the result looks like.
> > > It's typically a good idea to provide a link to a URL that contains
> > > the structure files from each stage of preparation, and the final
> > > result that exhibits the problem(s).
> > >
> > > Don't email your structure files to the list, just post them on the
> > > web somewhere and include a URL.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Tue, Sep 02, 2008 at 11:54:47AM -0700, Rabab Toubar wrote:
> > > > Hi,
> > > >
> > > > I am solvating a water molecule, and I always get the original water
> > > molecule outside the water box, and accordingly the water box dimensions
> > are
> > > different than the input. Would the position of the initial molecule
> > affect the
> > > rest of NAMD simulations? Or it is just a vmd visualization error ?
> > > >
> > > > Thanks
> > > > Rabab
> > > >
> > > >
> > >
> > > --
> > > 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/ <http://www.ks.uiuc.edu/%7Ejohns/> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > 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