VMD-L Mailing List

From: Jufang Shan (jufang.shan_at_gmail.com)
Date: Thu May 08 2008 - 11:26:38 CDT

John,

When I use 500, I get the same variations as without using the "-samples" flag.
PC: 21.49
ia64: 17.77
irix: 18.39

But the variations do decrease when I increase the number of samples.
Do you think the following variations are normal?
1000:
PC: 18.95
ia64: 16.47
irix: 17.77

5000
PC: 17.62
ia64: 18.22
irix: 18.58

Many thanks,
Jufang

On Thu, May 8, 2008 at 12:08 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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