metadynamics/ABF simulations using collective variables - issues with restarting the calculations

From: Marimuthu Krishnan (
Date: Tue Nov 13 2012 - 08:42:43 CST

Hello everybody,

While calculating free energies using the Collective Variable Module
implemented in NAMD 2.9, I noticed something unusual. Both ABF and
metadynamics calculations run perfectly fine when I perform new
calculations. When I try to restart my simulations (both for ABF and
metadynamics), I notice 4-5 fold decrease in performance (relative to a new
run) irrespective of the type of reaction coordinate (distance-based or
angle-based) used. These calculations were run on Kraken (NICS) and same
number of cores was used for both the fresh and restart runs. I do remember
that I did not have this problem before when using earlier versions of
NAMD. I would appreciate help from experts.

A related minor issue with naming of the restart file. One of the output
files from ABF/metadynamics is named file_rst.colvars.state.old but if you
want to restart a run using this old restart file, NAMD 2.9 expects its
name be file_rst.old.colvars.state. It would be useful if this mismatch in
names is fixed.


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