[gmx-users] ED analysis

Linda fuwei at adrik.bchs.uh.edu
Tue Sep 7 23:00:22 CEST 2004

Hi, Ruben, I am doing my ED analysis too, I am a little confused, could you tell how to get your cosine content of the other eigenvecors? Just simple by "g_analyze -f proj1_8.xvg -cc"? Could you give your calculated cosine value of 2-nd, 3-rd and 4-th eigenvector? 



Ooops! Sorry! I got it! Just read the manual...

Ruben M Buey wrote:

> No.
>> You should do:
>> g_anaeig -proj
>> (default is -last 8)
>> and then:
>> g_anaeig -f proj -cc
> g_anaeig -v eigenvec.trr -f beta_gdp_ca.xtc -s beta_gdp_ca.pdb -proj 
> proj1_8.xvg
> g_analyze instead g_anaeig?
> with
> g_analyze -f proj1_8.xvg -cc I only obtain:
> Cosine content of set 1 with 0.5 periods: 0.849278
> But what about the rest of eigenvectors??
> Thanks you,
> Cheers,
> Ruben
>> You will certainly get higher numbers for vectors 2-5.
>> Berk.
Best regards. 

Fu Wei

  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001   USA
  Phone:713-743-8355(o)  713-795-9270(h) 
  Email: fuwei at adrik.bchs.uh.edu

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