Molecular Dynamics P. Ojeda-May, B. Bryds, Y. Li, J. Eriksson Force fields
Umbrella Sampling String method Metadynamics
P. Ojeda-May, B. Brydsoe, J. Eriksson Error
= ()
JCP B, 109, 6714 (2005). WT Metadynamics error
PRL, 100, 020603 (2008) NaCl system
JCTC, 2018, Yi Yao and Yosuke Kanai NaCl system
PNAS, 99, 12562-12566 (2002) kcal/mol Ala-Dipeptide (Potential Energy
Scan)
Kinase system JACS, 131, 244 (2009)
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 (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 -n 16 -c 4 --cpu_bind=cores ./xthi
Hello from rank 0, thread 0, on b-cn1209.hpc2n.umu.se. (core affinity = 0) Hello from rank 0, thread 1, on b-cn1209.hpc2n.umu.se. (core affinity = 68) Hello from rank 0, thread 2, on b-cn1209.hpc2n.umu.se. (core affinity = 136) Hello from rank 0, thread 3, on b-cn1209.hpc2n.umu.se. (core affinity = 204) Hello from rank 1, thread 0, on b-cn1209.hpc2n.umu.se. (core affinity = 1)
Hello from rank 1, thread 1, on b-cn1209.hpc2n.umu.se. (core affinity = 69) Hello from rank 1, thread 2, on b-cn1209.hpc2n.umu.se. (core affinity = 137) Hello from rank 1, thread 3, on b-cn1209.hpc2n.umu.se. (core affinity = 205) Accelerated MD
Yaozong Li, P. Ojeda-May Umbrella Sampling String method
A prior knowledge of reaction coordinate needed Metadynamics
Accelerated MD (aMD) Replica exchange Self-guided Langevin dynamics
no prior knowledge needed Why aMD 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 aMD J. Chem. Phys., Vol. 120, No. 24, 22 June 2004
enhanced potential energy :original potential energy : boost potential energy E: reference energy, beyond which the potential is determined by , otherwise (determined by users). tuning factor and used to control the deepness of the modified potential basin .
Basic Idea of aMD Original all-atom force field
Modified force field by aMD Basic Idea of aMD J. Chem. Phys. 127, 155102 2007
The larger becomes, the closer the modified potential gets to the original potential. Basic Idea of aMD (parameter determination)
Edihed = Vdihed_avg + 0.3 Vdihed_avg , dehed = 0.3 Vdihed_avg/5, Etotal = Vtotal_avg + 0.2 Natoms , total = 0.2 Natoms , Edihed : the reference energy applying to all dihedral angles in the system Vdihed_avg : the average dihedral potential from cMD dehed : the acceleration factor controlling the dihedral angle boost potential
Etotal : the reference energy applying to all atoms Vtotal : the average total potential from cMD Natoms : the atomic number of the kinase system total : the acceleration factor controlling the total boost potential
Case study Chem. Sci., 2017, 8, 3453-3464
