[gmx-users] restarting from cpt and binary identical

Peter C. Lai pcl at uab.edu
Thu Apr 21 00:00:26 CEST 2011

I have a fairly stupid question about restart from a checkpoint and binary
identical messages, probably because I can't understand the doco.

When I restart (or extend) a double-precision run from a checkpoint involving 
either dlb or even a different decomposition count (say I changed the number of 
parallel threads), I get a message that says it restarted but the 
trajectory is not binary identical.

My question is: I assume this trajectory will continue from the last set of 
double-precision coordinates and velocities in the cpt file? What is the 
loss in precision/error propagation of the resulting trajectory as compared 
to if I started the entire run from the begining? (say I am extending my
trajectory from 1ns to 10ns). I guess I understand that both trajectories 
would be "equally valid" but not binary identical, but what does this mean
in terms of things like ultimate RMSD measurements and so forth? I don't
necessarily care that the two concatenated trajectory files will not cmp to

Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
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