[Dock-fans] cpu-hours for virtual screening

Scott Brozell sbrozell at rci.rutgers.edu
Thu Sep 17 17:36:37 PDT 2009


Hi,

On Wed, Sep 02, 2009 at 11:10:52AM -0400, Ben Keshet wrote:
> Scott Brozell wrote:
> >On Fri, Aug 28, 2009 at 02:39:46PM -0400, Ben Keshet wrote:
> >>Scott Brozell wrote:
> >>>On Mon, Aug 24, 2009 at 12:39:41PM -0400, Ben Keshet wrote:
> >>> 
> >>  Could working on Cygwin slow down processing?
> >
> >I dont use cygwin, but 
> >http://www.timesys.com/blogs/tim/vmware_cygwin
> >Here is another situation where a benchmark suite would be useful -
> >still on our todo list.  If you think this is the problem them you could
> >download some standard suite:  gooooggggle on cygwin benchmark
> >gives several.
> >
> >scott
> >  
> I tried flexible docking a tiny subset (11 structures) both with cygwin 
> and Linux (RHE 4).  The input files and the hardware are identical.  A 
> few quick observations:
> 1) cygwin was nearly 10 times slower (5120+-3250 sec compared to 
> 680+-514, +- is 1 SD). 
> 2) the scores were close but not identical.  The average difference was 
> 1.7, with one molecule as much as 7.  This led to differences in the 
> ranking of the ligands.
> 3) the average RMSD was above 5 angstrom, but excluding 2 ligands which 
> had an RMSD>10A, the RMSD was 2.9.  This number may be misleading in the 
> case of my receptor, since the binding site is composed of 6 parallel 
> sequence-identical chains, so in some cases the poses are "transposed" 
> along the chains while maintaining similar interactions.  Moreover, my 
> binding site is not very tight, so may be more challenging.
> 4) The number of conformations in linux (as indicated in the .out file) 
> was always lower than when using cygwin.  What could be the reason?

All this is not atypical as far as results comparisons between
platforms.  On the number of conformations, I have not recently
looked at the code, but in the past we have suggested that this is
due to the usual suspects: floating point math, etc;
see the (5) in
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation

> My own conclusion is that time-wise better to run on Linux.  I don't 
> know why the number of conformations was lower on linux, and what are 
> all the reasons for the differences in scores, poses and therefore 
> ranking (both installation passed well the installation test).
> 
> A slightly unrelated question - the number of orientations for all the 
> ligands was 1000, however the max_orientations parameter in the input 
> file is 500.  What am I missing?

Are you sure ?  

Scott



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