VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 22 2005 - 11:11:45 CDT

Hi,
  With VMD, you can extract as many parameters as you want in a
single pass since you can run arbitrary Tcl/Python. :-)

  John

On Fri, Apr 22, 2005 at 06:08:13PM +0200, Bogdan Costescu wrote:
> On Fri, 22 Apr 2005, Kos wrote:
>
> > Bogdan please explain what do you mean about CHARMM problems by 'I/O
> > bandwidth and passes' (examples HW)?
>
> There are cases when several distinct parameters (f.e. some phi
> angles) are required to be plotted against time. The "classical"
> approach is to extract only one parameter in each pass through the
> trajectory, such that for n parameters the trajectory is completely
> read n times from disk/network, if the trajectory is read one frame at
> a time. If the trajectory is read in memory before analysis, several
> such pases can be done on the data in memory, therefore no additional
> disk/network resources are used.
>
> Of course, for systems where the available memory is larger than the
> trajectory to be read, the operating system can do some caching and
> provide data much faster (also from memory, but a different "pool")
> than disk/network.
>
> --
> Bogdan Costescu
>
> IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen
> Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY
> Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868
> E-mail: Bogdan.Costescu_at_IWR.Uni-Heidelberg.De
> 

-- 
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