2014/5/21
2014年バイオスーパーコンピューティング・ソフト講習会シリーズ「CafeMol」粗視化分子モデル
計算ソフト講習会（実習編）

検崎博生
理化学研究所情報基盤センター

CafeMol (www.cafemol.org)• Features are;– Various CG models– protein/DNA/RNA– multiple basin model– accurate CG model– Simulating protein-at-work– “switching”• Under developmentlipid• Developer
検崎博生、古賀信康、藤原慎司、堀直人、金田亮、李 文飛、岡崎圭一、姚 新秋、寺川剛、伊藤真志保、高田彰二
京都大学高田研究室

CafeMol 2.1 (2013/7)
source & manual released

SCLS Supercomputer system• Supercomputational Life Science(SCLS)– HPCI戦略プログラム分野1「予測する生命科学・医療および創薬基盤」• K computer compatible• System– PRMEHPC FX10– 48nodes– CPU: SPARC64TMIXfx– Memory: 32GB/nodeHow to get CafeMol(SCLS)
1. log in SCLS supercomputer system
2. copy the /home/islim/cafemol/cafemol2.1_scls directory
3. read README, README_SCLS, and INSTALL files

cafemol2.1_scls directories
src: source files
para: parameter files
aicg: aicg-related files
pdb: sample PDB files
ninfo: sample ninfo files
example: sample input/output files

How to get CafeMol(general)
1. Access “http://www.cafemol.org”
2. Download the latest version of CafeMol
3. Extract it$ tar zxvf CafeMol_xxx.tar.gz
Extracted directories
src: source files
para: parameter files
aicg: aicg-related files
pdb: sample PDB files
ninfo: sample ninfo files
example: sample input/output files

How to make
1. $ cd src
2. $ vi Makefile
3. $ make clean
4. $ make

Editing Makefile• Uncomment the appropriate lines• For SCLS and K computer, ”#------ K computer” block is appropriate
FC = mpifrtpx
FC_UTIL = mpifrtpx
MPI parallelizationCPP = -DTIME –DMPI_PAR –DMPI_PAR2 –DMPI_PAR3 –DMPI_REP
INC = timing measurement
OPT = -Kfast, openmp OpenMP parallelization
LIB = optimization

How to execute CafeMol
Normal simulation$ ./cafemol [input-file]

MPI simulation(depend on system)$ mpirun –n [mpi-parallel-number] ./cafemol [input-file]

Restart simulation$ ./cafemol [input-file] [restart-file]

In case of error with “segmentation fault”$ ulimit –s unlimited

How to execute CafeMol(SCLS)$ pjsub ./sh3.sh
sh3.sh#!/bin/sh#PJM –L “rscgrp=small”
small, large, interactive#PJM –L “node=1”
small: 1-12nodes#PJM –mpi “proc=1”# of mpi parallelization#PJM –L “elapse=1:00:00”
small: -3:00:00#PJM –jmerge std output and stderr output
export OMP_NUM_THREADS=1 # of OpenMP parallelization

time ./mpiexec ./cafemol example/sh3/sh3/inp$ pjqstat$ pjdel [JOBID]

display job status(-A:all user)cancel job$ pjsub --interact
interactive job
e.g.
$ pjsub --interact –L “node=2” –mpi “proc=8”$ mpiexec ./cafemol cafemol_go_replica.sh$ exitExample files• Protein folding– sh3, sh3.sh(serial)• Restart simulation– sh3_restart• AICG2plus model– aicg2plus• Multi-basin model– gbp_mgo1• CG DNA model– dna130, dna130.sh(16 threads)• Protein/DNA system– p53_DNA_flexible_local• Replica exchange methods– cafemol_go_reprica, cafemol_go_replica.shInput file(essential block 1)<<<< filenames
path = ./dataoutput directory
filename = sh3
output file names up to the suffixOUTPUT psf pdb dcd rst list of output file extension name
path_pdb = ./pdb
directory of reference structures
path_ini = ./pdb
directory of initial structures
path_natinfo = ./ninfo
directory of native info files>>>><<<< job_cntl
i_run_mode = 2
2:constat T, 6:REMD
i_simulate_type = 1
1:Lengevin, 2:Berendsen, 3:Nose-Hoover
i_initial_state = 1
1:random, 2:native, 3:initial, 4:BDNA, 5:CG>>>><<<< unit_and_statei_seq_read_style = 1
1:PDB, 2:sequence, 4:CGi_go_native_read_style = 1 1:PDB, 2:native_info, 3:none
1 protein 1SRL.pdb
define unit(chain) and state(multi-basin)>>>>Input file(essential block 2)<<<< energy_function
LOCAL(1) L_GO
NLOCAL(1/1) GO EXV>>>>

local energy L_GO, L_AICG2_PLUS, L_BDNA
nonlocal energy GO, EXV, AICG2, DNA, ELE

multi-basin model<<<< energy_function
LOCAL(1a/1a) L_GO
LOCAL(1b/1b) L_GO
NLOCAL(1a/1a) GO EXVNLOCAL(1b/1b) GO EXVMULTIGO_SYSTEM(1a) 1a/1a
MULTIGO_SYSTEM(1b) 1b/1b>>>>

Input file(essential block 3)<<<< md_information
n_step_sim = 1
n_tstep(1) = 300000
tstep_size = 0.2
n_step_save = 100
n_step_neighbor = 100
tempk = 300.0
n_seed = 1>>>># of switching poteintial# of MD steps
time length in each MD step (0.05-0.2)
frequency of output
frequency of calculate neighboring list
temperature(K)random number seed(32-bit integer except 0)

Input file(optional block 1)<<<< initial_struct
1 1WDN_2b.pdb
initial file>>>><<<< multiple_gobdemax_mgo = 100.0
upper limit of the change in bond energybaemax_mgo = 1.0
upper limit of the change in bond angle energy
dihemax_mgo = 0.5
upper limit of the change in dihedral angle energy
ENEGAP(1)(1) 0.0 -1.8 value of DV at each state
DELTA(1ab) 28.0
value of D>>>><<<< electrostatic
cutoff_ele = 5.0
truncation distance(Debye length kD)ionic_strength = 0.2
ionic strength(M)diele_water = 78.0
dielectric constant(78 at 300K)>>>>

CafeMol utility• Calculation of RMSD$./cafe calc rmsd [reference-file] [trajectory-file] [output-file] (initial-number] [last-number])• Data conversion of restart file to text format$ ./show_rst [restart-file] > [text-format-restart-file]• Data conversion of text format restart file to binary file$ ./a2rst [text-format-restart-file] [restart-file]How to use VMD• Linux– $ vmd sh3.movie– $ vmd sh3.psf sh3.dcd• Windows– drug and drop sh3.movie to vmd icon
– drug and drop sh3.psf and sh3.dcd to vmd icon– run vmd
1. click [File]→[New Molecule…] in VMD Main
2. click [Browse…] in Molecule File Browser
3. choose sh3.psf and click load in Molecule File Browser
4. click [Browse…] in Molecule File Browser
5. choose sh3.dcd and click load in Molecule File Browser• Representation
1. click [Graphics]→[Representations…] in VMD Main
2. select [Drawing Method] “VDW” in Graphical Representation
3. change [Sphere Scale] “1.6” in Graphical Representation

実習で何をやるか• exampleをいろいろ実行してみて、結果をVMDで観る• exampleのinput fileを少し変更してみる••••

計算時間を長くする：n_tstep(1)を大きくする
温度を変える：tempkを低温にしたり、高温にする
初期構造を変える：i_initial_state=2にすると初期構造はPDB構造
乱数を変える：n_seedを0以外の整数に変える• 適当なタンパク質のfolding simulationをする
1. PDBからお望みのタンパク質のX線結晶構造をダウンロードして、pdbディレクトリに配置する
2. sh3.inpやaicg2plus.inpなどを書き換え、input fileを作る
3. ジョブスクリプトをsh3.shから書き換えジョブを投げる• anchor, bridge, pull, boxなどのオプションを使ってみる––

pullオプションを使って、タンパク質を引っ張ってunfoldさせる
boxオプションを使って、タンパク質の閉じ込め効果を調べる

Acknowledgement
CafeMol development has been supported by Researchand Development of the Next-Generation IntegratedSimulation of Living Matter, a part of the Development
and Use of the Next-Generation Supercomputer Projectof the Ministry of Education, Culture, Sports, Scienceand Technology.