Molecular Dynamics P OjedaMay B Bryds Y Li

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Molecular Dynamics P. Ojeda-May, B. Brydsö, Y. Li, J. Eriksson

Molecular Dynamics P. Ojeda-May, B. Brydsö, Y. Li, J. Eriksson

Force fields

Force fields

Umbrella Sampling

Umbrella Sampling

String method

String method

Metadynamics P. Ojeda-May, B. Brydsoe, J. Eriksson

Metadynamics P. Ojeda-May, B. Brydsoe, J. Eriksson

Error JCP B, 109, 6714 (2005).

Error JCP B, 109, 6714 (2005).

WT Metadynamics error PRL, 100, 020603 (2008)

WT Metadynamics error PRL, 100, 020603 (2008)

Na. Cl system JCTC, 2018, Yi Yao and Yosuke Kanai

Na. Cl system JCTC, 2018, Yi Yao and Yosuke Kanai

Na. Cl system PNAS, 99, 12562 -12566 (2002)

Na. Cl system PNAS, 99, 12562 -12566 (2002)

kcal/mol Ala-Dipeptide (Potential Energy Scan) Ψ Ф

kcal/mol Ala-Dipeptide (Potential Energy Scan) Ψ Ф

Kinase system JACS, 131, 244 (2009)

Kinase system JACS, 131, 244 (2009)

Accelerators GPU showing the independent units Streaming Multiprocessors (SM). Single tile KNL, composed of

Accelerators GPU showing the independent units Streaming Multiprocessors (SM). Single tile KNL, composed of several Tiles

NAMD files • . pdb coordinates • Parameter file • X-plor topology file •

NAMD files • . pdb coordinates • Parameter file • X-plor topology file • . namd (input for the simulation)

KNL Thread affinity #export OMP_PROC_BIND=spread, close, etc. #export OMP_PLACES=threads, cores, etc. export OMP_NUM_THREADS=4 srun

KNL Thread affinity #export OMP_PROC_BIND=spread, close, etc. #export OMP_PLACES=threads, cores, etc. export OMP_NUM_THREADS=4 srun -n 16 -c 4 --cpu_bind=cores. /xthi Hello from rank 0, thread 0, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 0) Hello from rank 0, thread 1, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 68) Hello from rank 0, thread 2, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 136) Hello from rank 0, thread 3, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 204) Hello from rank 1, thread 0, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 1) Hello from rank 1, thread 1, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 69) Hello from rank 1, thread 2, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 137) Hello from rank 1, thread 3, on b-cn 1209. hpc 2 n. umu. se. (core affinity = 205)

Accelerated MD Yaozong Li, P. Ojeda-May

Accelerated MD Yaozong Li, P. Ojeda-May

Umbrella Sampling String method A prior knowledge of reaction coordinate needed Metadynamics Accelerated MD

Umbrella Sampling String method A prior knowledge of reaction coordinate needed Metadynamics Accelerated MD (a. MD) Replica exchange Self-guided Langevin dynamics no prior knowledge needed

Why a. MD Fastly observe rare events that conventional MD cannot sample in a

Why a. MD Fastly observe rare events that conventional MD cannot sample in a feasible simulation time. no reaction coordinate needs to be defined a priori.

Basic Idea of a. MD J. Chem. Phys. , Vol. 120, No. 24, 22

Basic Idea of a. MD J. Chem. Phys. , Vol. 120, No. 24, 22 June 2004

Basic Idea of a. MD Original all-atom force field Modified force field by a.

Basic Idea of a. MD Original all-atom force field Modified force field by a. MD

Basic Idea of a. MD J. Chem. Phys. 127, 155102 2007

Basic Idea of a. MD J. Chem. Phys. 127, 155102 2007

Basic Idea of a. MD (parameter determination) Edihed = Vdihed_avg + 0. 3 ×

Basic Idea of a. MD (parameter determination) Edihed = Vdihed_avg + 0. 3 × Vdihed_avg , αdehed = 0. 3 × Vdihed_avg/5, Etotal = Vtotal_avg + 0. 2 × Natoms , αtotal = 0. 2 × Natoms , Edihed : the reference energy applying to all dihedral angles in the system Vdihed_avg : the average dihedral potential from c. MD αdehed : the acceleration factor controlling the dihedral angle boost potential Etotal : the reference energy applying to all atoms Vtotal : the average total potential from c. MD Natoms : the atomic number of the kinase system αtotal : the acceleration factor controlling the total boost potential

Case study Chem. Sci. , 2017, 8, 3453 -3464

Case study Chem. Sci. , 2017, 8, 3453 -3464