From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Thu Nov 22 2007 - 02:19:55 CST
> For different parallel runs, NAMD will perform non-deterministically, in the
> sense that the order of completion of different processors (and even the work
> that is assigned to them) will likely change, altering the order of summed
> energies. Due to the non-associativity of floating point addition, you should
> eventually see slightly different energy values from two parallel runs of an
> identical trajectory.
I thought the non-reproducibility of simulations in NAMD was mainly
because of the Berendsen pressure controller employed, which gives random
kicks to particles every few steps. Whether or not the run is parallel, I
do not think the trajectories will be reproducible, although I have not
tested this myself.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:35 CST