[gmx-users] RMSD VS. parallel simulation

[DeChang Li]

Dear all,

  I used Gromacs-3.3.1 to simulate a small protein in water.
I have used 2 and 16 CPUs to do the simulation respectively. But
I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs
simulation and 0.20 nm in the 16 CPUs one. Are these differences
reasonable?
  In the 16 CPUs simulation, the RMSD of protein at t=0 was about
0.1 nm, why not equal to zero? I used the initial structure for the
least squares fit.




Best regards,
2008-4-5


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Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China

Tel:   +86-10-62773779(O)
Email: lidc02 at mails.tsinghua.edu.cn
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