{"id":1360,"date":"2017-12-05T15:04:11","date_gmt":"2017-12-05T06:04:11","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=1360"},"modified":"2022-05-29T18:20:57","modified_gmt":"2022-05-29T09:20:57","slug":"gromacs%e3%81%ae%e6%b8%a9%e5%ba%a6%e3%81%ae%e8%a8%ad%e5%ae%9a%e3%82%92%e4%b8%80%e6%8b%ac%e5%a4%89%e6%9b%b4%e3%81%99%e3%82%8b%e3%82%b7%e3%82%a7%e3%83%ab%e3%82%b9%e3%82%af%e3%83%aa%e3%83%97%e3%83%88","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2017\/12\/05\/gromacs%e3%81%ae%e6%b8%a9%e5%ba%a6%e3%81%ae%e8%a8%ad%e5%ae%9a%e3%82%92%e4%b8%80%e6%8b%ac%e5%a4%89%e6%9b%b4%e3%81%99%e3%82%8b%e3%82%b7%e3%82%a7%e3%83%ab%e3%82%b9%e3%82%af%e3%83%aa%e3%83%97%e3%83%88\/","title":{"rendered":"Gromacs\u306e\u6e29\u5ea6\u306e\u8a2d\u5b9a\u3092\u4e00\u62ec\u5909\u66f4\u3059\u308b\u30b7\u30a7\u30eb\u30b9\u30af\u30ea\u30d7\u30c8"},"content":{"rendered":"

\u6e29\u5ea6\u30ec\u30d7\u30ea\u30ab\u4ea4\u63dbMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3059\u308b\u305f\u3081\u306emdp\u30d5\u30a1\u30a4\u30eb\u3092\u4e00\u62ec\u8a2d\u5b9a\u3059\u308b\u305f\u3081\u306e\u5099\u5fd8\u9332\uff0e<\/p>\n

Temperature generator for REMD-simulations<\/a>\uff082022\/5\/29\u3001\u30ea\u30f3\u30af\u5148\u5909\u66f4\uff09\u3092\u4f7f\u3063\u3066\uff0c\u30ec\u30d7\u30ea\u30ab\u6bce\u306e\u6e29\u5ea6\u3092\u8a08\u7b97\u3059\u308b\u3068\uff0c
\n\"\"
\n\u8868\u3068\u30ab\u30f3\u30de\u533a\u5207\u308a\u306e\u6570\u5024\u306e\u30ea\u30b9\u30c8\u3092\u5f97\u3089\u308c\u307e\u3059\uff0e<\/p>\n

310.00, 313.19, 316.34, 319.51, 322.72, 325.94, 329.06, 332.34, 335.64, 338.97, 342.31, 345.69, 349.09, 352.53, 355.98, 359.48\n<\/pre>\n
\u3053\u308c\u3092remd.txt<\/span>\u3068\u3044\u3046\u540d\u524d\u3067\u4fdd\u5b58\u3057\u3066\u304a\u304d\u307e\u3059\uff0e<\/p>\n
16\u500b\u306e\u30ec\u30d7\u30ea\u30ab\u3092\u52d5\u304b\u3059\u305f\u3081\u306b\uff0c\u30c7\u30a3\u30ec\u30af\u30c8\u30ea1,2,3,…,16\u3092\u4f5c\u6210\u3057\u307e\u3059\uff0e<\/p>\n
$ mkdir {1...16}<\/code><\/pre>\n
\u305d\u308c\u305e\u308c\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306bGromacs\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u8a2d\u5b9a\u304c\u66f8\u304b\u308c\u305fmdp\u30d5\u30a1\u30a4\u30eb (npt.mdp) \u3092\u30b3\u30d4\u30fc\u3057\u307e\u3059\uff0e<\/p>\n
$ (for dir in `seq 1 16`; do cp npt.mdp $dir; done)<\/code><\/pre>\n
\u3053\u306e\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e\u306e\u6e29\u5ea6\u306b\u95a2\u3059\u308b\u8a2d\u5b9a\u306f\uff0c\u4f8b\u3048\u3070temperature coupling\u30b0\u30eb\u30fc\u30d7\u304c2\u3064\u306e\u5834\u5408\uff0c\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u307e\u3059\uff0e\u8a2d\u5b9a\u6e29\u5ea6ref_t\u306b\u306f\u6570\u5024\u3067\u306f\u306a\u304fTEMP\u3068\u3044\u3046\u6587\u5b57\u5217\u304c\u5165\u3063\u3066\u3044\u307e\u3059\uff0e<\/p>\n
tcoupl      = V-rescale                 ; modified Berendsen thermostat\ntc-grps     = Protein Water_and_Ions    ; two coupling groups - more accurate\ntau_t       = 0.1   0.1                 ; time constant, in ps\nref_t       = TEMP   TEMP<\/pre>\n
\u3053\u306e\u6587\u5b57\u5217TEMP\u3092\u30ec\u30d7\u30ea\u30ab\u6bce\u306e\u6e29\u5ea6\u5024\u3067\u7f6e\u304d\u63db\u3048\u307e\u3059\uff0e<\/p>\n
\u4ee5\u4e0b\u306eshell script (remd.sh<\/span>\u3068\u3044\u3046\u540d\u524d\u306b\u3059\u308b) \u3092\u5b9f\u884c\u3057\u3066\uff0c\u5404\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u4e2d\u306emdp\u30d5\u30a1\u30a4\u30eb\u306e\u4e2d\u306e\u6587\u5b57\u5217TEMP\u3092\u9806\u756a\u306b\u7f6e\u304d\u63db\u3048\u307e\u3059\uff0e<\/p>\n
#!/bin/bash\nj=0\nfor L in `cat remd.txt | sed -e 's/,//g'`\ndo\n    j=`expr $j + 1`\n    sed -i.bak -e 's/TEMP/'$L'/g' $j/*.mdp\n    echo $j: $L\ndone<\/pre>\n
$ sh .\/remd.sh<\/code><\/pre>\n
$ grep ref_t *\/npt.mdp<\/code><\/pre>\n
\u3068\u3044\u3046\u30b3\u30de\u30f3\u30c9\u3067ref_t\u304c\u542b\u307e\u308c\u308b\u884c\u3092\u629c\u304d\u51fa\u3057\u3066\u78ba\u304b\u3081\u3066\u307f\u308b\u3068\u6e29\u5ea6\u304c\u66f8\u304d\u8fbc\u307e\u308c\u3066\u3044\u308b\u306e\u304c\u78ba\u8a8d\u3067\u304d\u307e\u3059\uff0e<\/p>\n
1/npt.mdp:ref_t       = 310.00 310.00                     ; reference temperature, one for each group, in K\n10/npt.mdp:ref_t       = 341.08 341.08                     ; reference temperature, one for each group, in K\n11/npt.mdp:ref_t       = 344.67 344.67                     ; reference temperature, one for each group, in K\n12/npt.mdp:ref_t       = 348.30 348.30                     ; reference temperature, one for each group, in K\n13/npt.mdp:ref_t       = 351.96 351.96                     ; reference temperature, one for each group, in K\n14/npt.mdp:ref_t       = 355.68 355.68                     ; reference temperature, one for each group, in K\n15/npt.mdp:ref_t       = 359.41 359.41                     ; reference temperature, one for each group, in K\n16/npt.mdp:ref_t       = 363.28 363.28                     ; reference temperature, one for each group, in K\n2/npt.mdp:ref_t       = 313.34 313.34                     ; reference temperature, one for each group, in K\n3/npt.mdp:ref_t       = 316.71 316.71                     ; reference temperature, one for each group, in K\n4/npt.mdp:ref_t       = 320.10 320.10                     ; reference temperature, one for each group, in K\n5/npt.mdp:ref_t       = 323.53 323.53                     ; reference temperature, one for each group, in K\n6/npt.mdp:ref_t       = 326.98 326.98                     ; reference temperature, one for each group, in K\n7/npt.mdp:ref_t       = 330.46 330.46                     ; reference temperature, one for each group, in K\n8/npt.mdp:ref_t       = 333.97 333.97                     ; reference temperature, one for each group, in K\n9/npt.mdp:ref_t       = 337.51 337.51                     ; reference temperature, one for each group, in K<\/pre>\n
Gromacs\u306e\u5b9f\u884c (\u30ec\u30d7\u30ea\u30ab\u4ea4\u63db\u306e\u5834\u5408)\uff0e<\/p>\n
$ (for dir in `seq 1 16`; do cd $dir; gmx grompp -f npt.mdp -c ..\/conf.gro -p ..\/topol.top -o md_01.tpr; cd ..; done)\n$ mpirun -np 16 mdrun_mpi -deffnm md_01 -multidir 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 -replex 500<\/code><\/pre>\n
mdrun_mpi\u306f\uff0cbuild-mdrun-only\u3068Open-MPI\u3092ON\u306b\u3057\u3066compile\u3057\u305f\u3082\u306e\uff0e\u30b9\u30d1\u30b3\u30f3\u3067\u306f “mdrun_mpi” \u306e\u4ee3\u308f\u308a\u306b “gmx_mpi mdrun”\uff0e\u81ea\u5206\u306e\u30b3\u30f3\u30d4\u30e5\u30fc\u30bf\u306e\u5c11\u306a\u3044\u30b3\u30a2\u6570\u3067\u591a\u304f\u306ereplica\u3092\u52d5\u304b\u3057\u305f\u3044\u6642\u306f\uff0c<\/p>\n
localhost slots=16<\/pre>\n
\u3068\u66f8\u304d\u8fbc\u3093\u3060\u30d5\u30a1\u30a4\u30eb (my-hosts) \u3092\u4f5c\u3063\u3066\u304a\u3044\u3066\uff0c<\/p>\n
$ mpirun --hostfile my-hosts -np 16 mdrun_mpi -deffnm md_01 -multidir 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 -replex 500<\/code><\/pre>\n
\u3068\u3059\u308b\u3068\u52d5\u304f\uff0e<\/p>\n
(\u4e86)<\/p>\n","protected":false},"excerpt":{"rendered":"
\u6e29\u5ea6\u30ec\u30d7\u30ea\u30ab\u4ea4\u63dbMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3059\u308b\u305f\u3081\u306emdp\u30d5 …<\/p>\n","protected":false},"author":1,"featured_media":1361,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"ja","_original_post":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=1360","footnotes":""},"categories":[5],"tags":[],"class_list":["post-1360","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a.png",1544,462,false],"thumbnail":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a-150x150.png",150,150,true],"medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a-300x90.png",300,90,true],"medium_large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a-768x230.png",768,230,true],"large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a-1024x306.png",800,239,true],"1536x1536":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a.png",1536,460,false],"2048x2048":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a.png",1544,462,false],"onepress-blog-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a.png",300,90,false],"onepress-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a.png",480,144,false],"onepress-medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/12\/d47004af638eccd73ea31d0222ba484a.png",640,192,false]},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":0,"uagb_excerpt":"\u6e29\u5ea6\u30ec\u30d7\u30ea\u30ab\u4ea4\u63dbMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3059\u308b\u305f\u3081\u306emdp\u30d5 ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1360","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=1360"}],"version-history":[{"count":20,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1360\/revisions"}],"predecessor-version":[{"id":3572,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1360\/revisions\/3572"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media\/1361"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=1360"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/categories?post=1360"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/tags?post=1360"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}