Why NAMD run Slow down

From: Ramin Omidvar (romidvar_at_gmail.com)
Date: Fri Sep 17 2010 - 11:32:07 CDT

Dear Namd Users

I'm running SMD simulation(constant pulling force) on a protein and running
speed was good.
After a couple of hours... Running speed goes down and down.
At the beginning , speed was about "1000Steps per Two Minute" but now it's
about "1000Steps per Two Hours".
My system specifications are:
NAMD Version: NAMD for CUDA 2.7b2
Operating System: Red Hat Enterprise Linux 5.1
CUDA Version: 2.3
RAM: 24GB
GPUs: 4x Tesla C1060
CPUs: Intel Xeon 5550

Material Specifications are:
A chain of CNTN4 (four IGs) solved in a Water Box and Ions
Force is applied on center of mass
 My conf.file is as same as Namd-tutorial file(for 2.7b2) except none rigid
bonds. May it relate to my configuration parameters?

Is there anybody else have had a same experience?
How can I check what is wrong?

Any help or hint is appreciated

Best regards
Ramin Omidvar
PhD student of Biomedical Engineering Dept.
AmirKabir University of Tech.
https://sites.google.com/site/romidvar

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