AMBER Archive (2003)

Subject: results of MD comparison

From: Xiaoqin Huang (xiaoqin_at_csit.fsu.edu)
Date: Wed Feb 26 2003 - 09:08:59 CST

Hello,
I have a question about the parallel mode of amber, that is:
when I compare the MD results (just 20 ps) of both the parallel mode (4 CPUs)
and the single running, the RMSD data is different greatly, and also the
total energy, the potential and kinetic energy of the whole system. it seems
these two runnings are on different directions, and the RMSD of parallel mode
is more fluctuating than the single one's.
The solvated systems are the same (about 15000 atoms), and with the same mdin
conditions. how can I explain these results?, which one should I select?
My computing environment is the PC cluster with Linux operation system and
typical MPI.
do you have any suggestions? thank you very much!
 

Xiaoqin Huang
School of Computation Science and Information Technology
Florida State University
Tallahassee, FL32306
U. S. A.
Tel: 850-644-5792(O)
Fax: 850-644-0098
E-mail: xiaoqin_at_csit.fsu.edu