VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 07 2008 - 23:08:22 CDT

Jufang,
  If you end up seeing noteworthy variations with 500 samples, then
I'd appreciate it if you can send me a copy of the structure in
question.

Thanks,
  John Stone

On Thu, May 08, 2008 at 12:04:19AM -0400, Jufang Shan wrote:
> Hi John,
>
> I am using 1.8.6 and I am loading exactly the same single structure using
> the same script.
>
> I will use 500 to see whether I get the same results.
>
> Many thanks,
> Jufang
>
> On Wed, May 7, 2008 at 5:59 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > Which version of VMD are you using?
> > You should definitely be using more than 50 samples, that is far
> > too low for accurate results, normally one would use 500 or more.
> >
> > Another question is whether you're using exactly the same structures
> > in your comparisons. Are you loading a single structure
> > (e.g. PDB) or are you loading a trajectory? Be sure you're comparing
> > identical frames etc.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, May 07, 2008 at 04:52:47PM -0400, Jufang Shan wrote:
> > > Hi,
> > >
> > > I have been using the same script to calculate sasa on different
> > machines
> > > (platforms) but got different results. I was wondering has anyone
> > encounter
> > > similar problems before.
> > > For some residues, the difference is bigger; for some, small.
> > >
> > > Here is the sasa-calculation script:
> > > set sel [atomselect top "protein or lipids"]
> > > set surf [atomselect top "segid A2 and resid 342"]
> > > set sasa [measure sasa 1.4 $sel -points pts -restrict $surf]
> > > #set sasa [measure sasa 1.4 $sel -points pts -restrict $surf -samples
> > 50]
> > >
> > > Here is the result if I turn off flag "-samples 50". x86_64 gives the
> > same
> > > result as ia64.
> > > PC: 21.49
> > > ia64: 17.77
> > > irix:18.39
> > >
> > > The result is still different when I change the probe to 1.0
> > > PC: 29.3
> > > ia64:24.5
> > > irix: 25.7
> > >
> > > The result is also different when I use flag "-samples 50"
> > > PC: 26.94
> > > ia64: 13.39
> > > iris:25.47
> > >
> > >
> > > Best,
> > > Jufang
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> > 

-- 
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