VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 25 2009 - 23:34:08 CDT

Hi all,
  Most likely as psfgen continues to evolve, we would begin storing
the diagnostic information that's being printed as part of the
generated structure data. I can tell you that in our recent efforts
building the 100+ million atom BAR domain test system for Blue Waters
that no human would ever want to read a plain text version of this
info, even if stored in a log file.. :-) Just the log from a solvate
run on a 116M atom test system was gargantuan. The psfgen code already
stores some information in optional data fields with the structure, we'll
likely want to continue building up that capability.

Cheers,
  John

On Wed, Mar 25, 2009 at 06:17:19PM -0400, Axel Kohlmeyer wrote:
> On Wed, 2009-03-25 at 23:11 +0200, Thomas Evangelidis wrote:
> > Hi everyone,
> >
> > is there any way to prevent psfgen from printing warning messages,
> > explicitly or implicitly (using tcl synstax)?
> > My console is filled up with messages like this:
> >
> > Warning: explicit angles in residue TIP3:8721 will be deleted during
> > autogeneration
> >
> > and I have the feeling that they slow down my calculations.
>
> ...only if you use tkcon. do you?
>
> there should be a way to do it generally. one can probably (ab)use the
> infrastructure that i programmed in the VMDCON patches in the current
> cvs code, those are, however, not yet compiled into the normal
> distribution and i have not thought about how to cleanly implement
> a way to silence this kind of console output in a clean fashion.
> i'd probably have to convert the whole psfgen module to use the
> prioritized output from vmdcon.C. hmmm...
>
> something along those lines will, in fact, be needed for anybody running
> tcl commands on the console (even text mode) on large systems.
>
> cheers,
> axel.
>
> >
> > thanks,
> > Tom
>
> --
> =======================================================================
> 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. 

-- 
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