GENESIS Hands-on Part 2-2:
High performance computation with GENESIS
Jaewoon Jung
RIKEN Center for Computational Science
2024/07/01
IUPAB2024 Hands-on Training Program CHARMM-GUI/GENESIS MD Tutorial
1

Schedule of GENESIS parts (6/30-7/2)
06/30 Part1
13:30 – 15:00

GENESIS basics and GENESIS on Fugaku (Kobayashi) Lecture
Hands-on tutorial on Fugaku

07/01 Part 2
14:30 – 15:30

Coarse-grained simulations in GENESIS (Tan)

15:30 – 16:30

High-performance computation with GENESIS (Jung)

07/02 Part 3
13:30 – 15:00

Generalized-ensemble simulations using GENESIS (Ito)2Contents• Decision of Nonbonded interaction scheme• Large time step integration with Hydrogen
Mass Repartitioning• Others3Force calculation for biological systems
Force can be divided into bonding and nonbonding interactions.
Bond (ex. 1-2, 2-3, …)𝐸!"#$%#&'( = # 𝑘, 𝑏 − 𝑏- .
)"%*+.

Angle (ex. 1-2-3, 2-3-4,..)

𝑘4 1 + 𝑐𝑜𝑠 𝑛𝜑 − 𝛿Dihedral (ex. 1-2-3-4, …)+ # 𝑘0 𝜃 − 𝜃1234'%/($+…

+5
Hydrogen: Light Gray
Carbon: Dark Gray
Oxygen: RedNitrogen: Blue#*&1$*2'(3+#%"%5)"%*$*!'&2+869
𝜀67:&%
𝑅67𝑟67;.

−:&%
𝑅67𝑟67van der Waals(ex. 1-5, …) :<𝑞6 𝑞7+𝑟67

Coulomb(ex. 1-5, …) :BondingO(N)Nonbonding
O(N2)

4

Nonbonded interactions• Nonbonded interactions (Coulomb + vdW) are the main bottleneck ofsimulations.
• Nonbonded interactions are divided into those of real spacewith cutoff-distance and reciprocal lattice space.
#869
𝜀6767,𝐧:&%𝑅67𝑟67,𝐧;.

−:&%𝑅67𝑟67,𝐧<𝑞6 𝑞7+→ #𝑟67,𝐧869
𝜀6767,𝐧?!" @A#:&%𝑅67

𝑟67,𝐧Real space calculation
;.

−:&%
𝑅67

<𝑟67,𝐧𝑞6 𝑞7 erfc(𝛼𝑟67,𝐧 )＋𝑟67,𝐧Fi-th particle

1exp( − 𝜋 . 𝐤 . /𝛼 . )
𝛼.
.
#𝑆(𝐤)
−
#
𝑞62𝜋𝑉
𝐤.
𝜋
𝐤C𝟎6E;

Reciprocal space calculation

Range of j-th particle thatinteracts with i-th particle

5

Nonbonded interaction kernels in GENESIS• In GENESIS, there are four interaction kernels for real space nonbondedinteraction.
1. Generic2. Fugaku

3. Intel

4. GPU• Please choose the best calculation kernel from MD with small simulation
time (We will do at this time).
• We also have four reciprocal space calculation schemes.
• Reciprocal space calculation scheme is decided by GENESIS by executing
each scheme before starting MD.
6

Contents• Decision of Nonbonded interaction scheme• Large time step integration with Hydrogen
Mass Repartitioning• Others
7Hydrogen Mass Repartitioning (HMR) scheme

Hopkins et al., JCTC. 11, 1864 (2015))
J. Jung et al., JCTC. 17, 5312 (2021))• Increase the mass of hydrogen atoms while reducing the mass of heavyatoms such that the total mass of one hydrogen group is not changed.
• With the HMR scheme, we can avoid the problem of SHAKE/RATTLE error by
reducing the displacement of hydrogen atoms.
• We increase the mass of the hydrogen atoms three times.

8

HMR increases the stability (example of energy drift)• HMR reduces the energy drift and increases the overall stability.
J. Jung et al., JCTC. 17, 5312 (2021))
9

Accurate temperature/pressure evaluation isimportant for large time step!!

J. Jung et al., JCTC, 15, 84 (2019))
J. Jung et al., JCP, 153, 234115

Conventional temperature andpressure evaluation

Accurate temperatureand pressure evaluation
10in GENESISContents• Decision of Nonbonded interaction scheme• Large time step integration with Hydrogen
Mass Repartitioning• Others
11

Multiple time step integration
We can reduce the computational cost by skipping slow motion force every other step

1𝑡 − ∆𝑡
2𝑡 − ∆𝑡𝑡 +2∆𝑡

𝐪 𝑡 + ∆𝑡 → 𝐪 𝑡 + 2∆𝑡𝐪 𝑡 + 2∆𝑡 → 𝐪 𝑡 + 3∆𝑡

𝐅+("G (𝑡)H 𝑡𝐩 𝑡 →𝐩𝐅+("G (𝑡 + 2∆𝑡)
JH 𝑡 + 2∆𝑡 → 𝐩 𝑡 + 2∆𝑡𝐩𝐅+("G (𝑡 + 2∆𝑡)
H 𝑡 + 2∆𝑡
𝐩 𝑡 + 2∆𝑡 → 𝐩

1→ 𝐩 𝑡 + ∆𝑡2

𝐅#%&' (𝑡)3𝑡 + ∆𝑡
2𝑡 + ∆𝑡𝐪 𝑡 → 𝐪 𝑡 + ∆𝑡

H 𝑡
𝐩𝐅!"#$ (𝑡)1𝑡 + ∆𝑡2𝑡

3
1𝐩 𝑡 + ∆𝑡
𝐩 𝑡 + ∆𝑡𝐩 𝑡 + ∆𝑡
3
22→𝐩𝑡+∆𝑡
J→ 𝐩 𝑡 + ∆𝑡
H 𝑡 + 2∆𝑡→𝐩2𝐅!"#$ (𝑡 + ∆𝑡)

H 𝑡 + 2∆𝑡
𝐩
5
→ 𝐩 𝑡 + ∆𝑡
2𝐅!"#$ (𝑡 + 2∆𝑡)
𝐅#%&' (𝑡 + 2∆𝑡)

5𝐩 𝑡 + ∆𝑡
2→ 𝐩 𝑡 + 3∆𝑡𝐅!"#$ (𝑡 + 2∆𝑡)12