performance drop during run

From: Chitrak Gupta (
Date: Fri Jul 29 2016 - 10:41:32 CDT


I am running a simulation of a peptide in implicit solvent (generalized
born), and I am seeing a strange performance drop *during the run*. The
initial estimates by NAMD are ~ 125ns/day for a 560 atom system on a HPC
using 1 node, 16 processors. But after 24 hours there is only ~ 36ns worth
of data.

Has anyone faced this problem before?


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