VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 30 2009 - 12:55:28 CST

Lixia,
  Great, I'm glad you got it working.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 30, 2009 at 11:53:37AM -0700, Lixia Jin Day wrote:
> John and Alex,
>
> Thank you for replay. I used VMD1.8.6 and NAME2.6. I checked the log file
> after I sent the email yesterday and it said the simulation became
> unstable. I probably applied too dramatic forces to the molecule. I
> started from the very beginning more carefully this morning. I am in the
> middle of the simulation now.
> Thank you very much for helping.
>
> Lixia
>
> On Wed, Dec 30, 2009 at 11:39 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> We need much more information than what you've provided.
> Which program is giving you the error message you provided, was that VMD
> or
> NAMD that printed that message? If it was VMD, was the NAMD side of the
> connection still running, or did the NAMD process stop? Do you get any
> errors
> or warnings from the NAMD side of the link? Which versions of VMD and
> NAMD
> are you running, and on which platforms?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Tue, Dec 29, 2009 at 04:42:57PM -0700, Lixia Jin Day wrote:
> > I ran it well for several time today. But now it won't work. I
> turned of
> > VMD and load the molecule again and it still won't work. I
> restarted the
> > computer and it still won't work.
> > It does minimization for some steps (or finished), but it won't run
> the
> > simulation. It says:
> > " IMD connection ended unexpectedly; connection terminated. "
> >
> > I don't understand why.
> >
> > Do you have any idea about it?
> > Thank you !
> >
> > Lixia
>
> --
> 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
>
> --
> http://public.fotki.com/lily1907/ 

-- 
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