metadynamics simulations slow down and down

From: OiniL (
Date: Sat Sep 25 2010 - 23:06:17 CDT

Dear Namd Users:

I'm using metadynamics to simulate the folding of a protein with NAMD.

After several hours... Running speed got more and more slower.

The speed at the beginning was
 "CPU: 2.30465, 0.00455531/step Wall: 2.30378, 0.00455352/step,"
but 10 hours later, it's
 "CPU: 165525, 0.0223486/step Wall: 165964, 0.0223666/step,"

about 1/5 the speed at the beginning.

I tested another equilibrium run with the conf.file totally same as the
metadynamics file except the part of colvars, and this time the speed looks
fast and stable.

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

Any help or hint is appreciated
Best regards!

Cheng TAN
PhD student of Biophysics Dept.

Nanjing University


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