**From:** David Hardy (*dhardy_at_ks.uiuc.edu*)

**Date:** Thu Nov 22 2007 - 07:35:01 CST

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You can control the sequence of random numbers generated by choosing

the seed (although I don't know the method that NAMD employs to

generate random numbers in parallel). This part of the algorithm is

deterministic.

My earlier comment actually applies to NVE simulation with no "random"

component. Since Hamiltonian systems are chaotic, any small

perturbation (from the non-associativity of addition) can cause

deviation from a previous trajectory.

-Dave

On Nov 22, 2007, at 2:19 AM, Himanshu Khandelia wrote:

*>> Hi,
*

*>
*

*>> 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.
*

*>
*

----------------------------------------------------------

David J. Hardy, PhD

Theoretical and Computational Biophysics

Beckman Institute, University of Illinois

dhardy_at_ks.uiuc.edu

http://www.ks.uiuc.edu/~dhardy/

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