From: Brian Bennion (bennion1_at_llnl.gov)
Date: Fri May 08 2009 - 14:20:39 CDT
Hello,
I am wondering if anyone will comment on the ramifications of the following
two papers on NAMD2.6 and the current NAMD2.7b1 code. It would be nice to
have this response on the open list for future reference.
First, seeds for pseudo-random-number-generators (PRN0G) were shown to have
effects on stochastic forces under certain conditions such as rapid
restarts.
I know that NAMD is less vulnerable here than other packages but I don't
fully understand.
Cerutti, D. S.; Duke, R.; Freddolino, P. L.; Fan, H.; Lybrand, T. P. A
Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and
Andersen Dynamics J. Chem. Theory Comput. 2008, 4, 1669-1680
http://pubs.acs.org/doi/abs/10.1021/ct8002173
Second, this paper shows synchronization of supposedly separate trajectories
if seeds are not chosen properly and has definite consequences in REMD.
Even programs that use the clock as a source for the seed could be affected
by this problem if seed "requests" occur faster than the clock can propagate
to the next time point.
http://pubs.acs.org/doi/full/10.1021/ct800573m
Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory
Synchronization in Biomolecules
Any comments from developers/users would be helpful
Thank you
Brian Bennion
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