Replica Exchange MolecularDynamics (REMD) for Amber’sParticle-Mesh Ewalds MD (PMEMD)codeLia BallTeresa Head-Gordon GroupGoal: Converging Aβ monomerMolecular Dynamics simulations• Use Amber ff99SB force fieldand TIP4P-ew explicit watermodel to sample an all-atomrepresentation of Aβconformational ensemble• High temperature simulationsallow sampling of minimaseparated by large energybarriers• Replica Exchange MolecularDynamics (REMD) runsseveral independent simulationsrun at different temperatures inparallelREMD from 450 K to 287 K• Run PMEMD simulationsindependently for allreplicas• Every picosecond ofsimulation time attempt toexchange two replicas thatare close in temperature• Energy minima accessed athigh temperature willexchange down to the lowtemperature replica overtime450 K287 K final ensemblesync syncPMEMD is faster than Sander• PMEMD is a version of Sander MD code that is optimized to performparallelized particle-mesh Ewalds calculations, which use Fast-FourierTransforms to calculate the long-range forces on atoms.• On 16 processors, PMEMD takes 33 s to perform 1ps of simulation on one25,000 atom system including setup, Sander takes 55 s. If exchanges andsynchronization time are less than 22 s, my code will be faster than SanderREMD.• Exchange criteria are monte-carlo criteria that depend only on replicatemperatures and energies. Structure information does not need to betransferred between processors.Subroutine Organizationpmemdmaster_setupbcast_*_datrep_setupexchangeget_cmdlinerunmdpme_forcecheck_my_atom_movementcheck_new_list_limitdistribute_crdsMd_setupInstead of one master task, I create a master for each replica that doeseverything that the master does in the original code. Each master has its ownset of global variables that are never shared with the other replicas.Light blue boxes indicate subroutines that I modified from the original code,but that are still only run once for the entire program. Pink subroutines arethose that I modified and now separately for each replica.Amyloid β peptide structural ensembleand Alzheimer’s DiseaserrFawzi, N. L. et al J. ofMol. Biol. 2007, 365535-550.Computationally sampling the entire Aβmonomer conformational ensembleallows us to calculate average inter-hydrogen distances, which can becompared to NMR data.Knowing what structural elements Aβtransiently adopts as a monomer helps usto understand how the Aβ oligomers thatare believed to cause Alzheimer’s diseaseare
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