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
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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:08 CST