AMBER Archive (2002)

Subject: atomicfluct in ptraj

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Wed Dec 18 2002 - 17:16:29 CST

Hello all,

Had a question about the calculation of atomic fluctuation in ptraj. I wanted
to compare the Bfactors for the CA's of my protein in 50ps subsets of a 300ps
trajectory to each other and to Bfactors calculated for the whole traj, as one
indication that the system is equilibrating. When I did this, the resulting
Bfactors for the enitire 300ps run were larger than the average of the 6
subsets. Does this sound right? Can the whole thing be more than the avererage
of its parts? Would this possibly reflect some kind of net movement?

Below is my ptraj input file, and the first few lines of the output for
CA1-6.apf (whole 300ps) and CA1-6avg.apf (which I calculated by averaging the
6 50ps subsets: CA1.apf, CA2.apf, etc.).

Thanks,

Kristina

*****PTRAJ INPUT*******
NOTE: dataEXP1-5.crd contains the first 5 50ps blocks already pieced together
in an earlier ptraj session

trajin dataEXP1-5.crd
trajin dataEXP6.crd
reference dimerEXP.pdb
strip :BOG
strip :SPC
strip :ACD
strip :HEM
rms reference out rms1-6 @CA,C,N
atomicfluct out CA1-6.apf @CA byatom bfactor
atomicfluct out all1-6.apf byatom bfactor
atomicfluct out CA1.apf @CA start 1 stop 50 byatom bfactor
atomicfluct out CA2.apf @CA start 51 stop 100 byatom bfactor
atomicfluct out CA3.apf @CA start 101 stop 150 byatom bfactor
atomicfluct out CA4.apf @CA start 151 stop 200 byatom bfactor
atomicfluct out CA5.apf @CA start 201 stop 251 byatom bfactor
atomicfluct out CA6.apf @CA start 251 stop 300 byatom bfactor
atomicfluct out all1.apf start 1 stop 50 byatom bfactor
atomicfluct out all2.apf start 51 stop 100 byatom bfactor
atomicfluct out all3.apf start 101 stop 150 byatom bfactor
atomicfluct out all4.apf start 151 stop 200 byatom bfactor
atomicfluct out all5.apf start 201 stop 251 byatom bfactor
atomicfluct out all6.apf start 251 stop 300 byatom bfactor
go

*****CA1-6.apf*****

      1 34.892101
      2 17.341350
      3 11.668477
      4 9.323540
      5 8.187171
      6 9.064189
      7 11.077648
      8 14.017268
      9 13.443498
     10 10.562475

****CA1-6avg.apf****

      1 24.308553
      2 12.623209
      3 8.903701
      4 7.710983
      5 5.839279
      6 5.981133
      7 7.083099
      8 6.887985
      9 6.281120
     10 4.129294

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu