VMD-L Mailing List

From: Jufang Shan (jufang.shan_at_gmail.com)
Date: Wed May 07 2008 - 23:04:19 CDT

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
>