VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 02 2003 - 15:30:39 CDT

Dear Joe,
  Yes, there was a bug in VMD itself which was causing Thomas' script
to eat memory as it ran. Justin found and fixed this bug in the current
source tree, and I hope to have new test binaries with this fix in them
available shortly... I'll let you know when they are posted so you can
try them as well.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 02, 2003 at 03:23:54PM -0600, Joe Huang wrote:
> Dear Justin,
> Actually, I haven't really solved the problems yet about the "Memory
> problems with TCL scripts in VMD" that I mentioned on Thu Mar 20 2003
> -13:02:48 CST. So I wonder what you mean by saying that you have found
> and corrected the problem that was leading to the out of memory
> condition from Thomas' script. Do you mean there is a bug in the
> program and you have debugged it or ...?
>
> Best regards,
>
> H.-C. (Joe) Huang
>
> --
> *****************************************
> Hung-Chung Huang, M. T., M. Sc., Ph. D.
> Department of Biology and Biochemistry
> University of Houston, Houston, TX 77204
> Tel: (713) 743-8365, Fax: (713) 743-8351
> e-mail: HCHuang_at_uh.edu
> http://prion.bchs.uh.edu/~jhuang
> *****************************************
>
>
> Justin Gullingsrud wrote:
>
> >Thomas,
> >
> >Thanks for letting us know about this problem. We've found and corrected
> >the problem that was leading to your out of memory condition.
> >
> >I might also suggest:
> >
> >
> >
> >>proc rmsd_resid { frame } {
> >>
> >> global time_betw_frame selection rmsd_selec fid20 reference1 num_resid
> >>
> >> # the selection and frame used for fitting
> >> set compare1 [atomselect top $selection frame $frame]
> >>
> >>
> >
> >Since compare1 is always the same selection, just with a different frame
> >it will be much faster to create compare1 only once, then call
> >
> > $compare1 frame $frame
> >
> >to set the frame. This will also make it unnecessary to delete the
> >selection
> >below.
> >
> >
> >
> >> # compute the transformation
> >> set trans_mat1 [measure fit $compare1 $reference1]
> >>
> >> $compare1 delete
> >> unset compare1
> >>
> >>
> >
> >Cheers,
> >Justin
> >
> >
> >
>
> 

-- 
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