{"title":"Study on Parallel Processing of ab initio Crystal Orbital Calculations Using PC Cluster","authors":"H. Teramae, K. Ohtawara","doi":"10.2477/JCHEMSOFT.8.55","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.8.55","url":null,"abstract":"メッセージパッセンジャーとしてMPI(Message Passing Interface)の一種であるLAM(Local Area Multicomputer)を用いた、並列計算機環境の構築について述べる。実際の計算としては、一次元ポリマーのエネルギーバンド計算の並列処理について示した。PCとしては、Pentium IIIデュアルCPU仕様のマザーボードを使用したパーソナルコンピューター8台(CPU数は16)からなるPCを100BaseTの8ポートスイッチを使用してネットワーク接続を行い、クラスター構成とした。Poly-tetrafluoro-ethylene (C2F4)x の計算では8CPU使用時で実時間が6.27倍に加速された。Poly-(para-phenylene sulfide)(C6H4SC6H4S)xの計算ではクラスター全体のメモリーに二電子積分を全て置く事が可能となったために、8CPU使用時に約20倍という実時間の高速化が達成され、実時間の短縮という面においても並列処理は非常に有効であることがわかった。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2002-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128411112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The graph digitizer “GetValue" which assists in electrochemical analysis was programmed in Visual Basic language. The program has two subroutines of electrochemical analyses. One is for the estimation of diffusion coefficient using Cottrell's equation. The other is for the battery analysis using the plot of current vs. voltage. After digitizing a chart, the user can analyze obtained data by each method. The program can also be used as the standard graph digitizer that assists in obtaining numerical data from a chart on paper. A function that makes two specific points horizontal is equipped with the program to correct the inclination of the image. Specified points can be obtained in seven series. Numerical data are displayed in a table, and can be transferred to the clipboard. Either specified or interpolated methods can be selected, which enabled the efficient obtaining of numerical data.
{"title":"GetValue for Windows-電気化学測定解析を実装したグラフデジタイザの開発","authors":"英伸 城石, 悠城 鏑木, 瀬尾 美智子, 澄男 時田, 正夫 金子","doi":"10.2477/JCHEMSOFT.8.37","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.8.37","url":null,"abstract":"The graph digitizer “GetValue\" which assists in electrochemical analysis was programmed in Visual Basic language. The program has two subroutines of electrochemical analyses. One is for the estimation of diffusion coefficient using Cottrell's equation. The other is for the battery analysis using the plot of current vs. voltage. After digitizing a chart, the user can analyze obtained data by each method. The program can also be used as the standard graph digitizer that assists in obtaining numerical data from a chart on paper. A function that makes two specific points horizontal is equipped with the program to correct the inclination of the image. Specified points can be obtained in seven series. Numerical data are displayed in a table, and can be transferred to the clipboard. Either specified or interpolated methods can be selected, which enabled the efficient obtaining of numerical data.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"34 4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2002-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121157758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2001-12-31DOI: 10.14827/JCCJ1999.13.251
Zunyao Wang, Toshio Watanabe, O. Kikuchi
{"title":"Ab initio and DFT Calculations of Tetrachlorodibenzo-p-dioxins","authors":"Zunyao Wang, Toshio Watanabe, O. Kikuchi","doi":"10.14827/JCCJ1999.13.251","DOIUrl":"https://doi.org/10.14827/JCCJ1999.13.251","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"123 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132323596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
栄一 赤穂, G. Morris, D. Goodsell, David Wong, A. Olson
The capability to propose feasible ways of binding a putative ligand inhibitor to a known receptor site is crucial to the successful structure-based drug design. A computer docking approach is to position or “dock" ligand and receptor molecules together in many different ways and then score each orientation by applying a reasonable evaluation function. AutoDock3.0 is an unbiased type docking program in which a user does not have to direct a ligand to an active site, but the system finds an optimal position after a ligand is placed in a random manner. Synthesized derivatives of the intact inhibitor (inh1) of HIV protease were investigated for their docking modes as compared with their Ki values. Among the derivatives, inh3trans and inh6H were found to be more powerful inhibitors of HIV protease than the others. Gibbs free energy calculated by applying molecular mechanics interaction energies was compared with the one obtained by using experimental inhibitory potencies for a series of HIV protease inhibitors, and a fairly good correlation was found between the two. Based on this favorable correlationship between the computational and the experimental results, the computational experiments were pursued for the compounds drawn by Sybyl taking into consideration the fact that unexploited carbon affinity regions (or hydrophobic regions) with sizable volume were detected on the docking study of inh1 and inh8 against HIV protease. Those were compounds with a t-butyl substituted by various hydrophobic side chains. Among those a compound with a benzyl group exhibited the lowest docking energy. Since one of the goals of this paper was to perform the computational drug-design experiment to investigate potential HIV protease inhibitors, the authors would like to leave the clinical investigational work for the expertise of those areas.
{"title":"A Study on Docking Mode of HIV Protease and Their Inhibitors","authors":"栄一 赤穂, G. Morris, D. Goodsell, David Wong, A. Olson","doi":"10.2477/JCHEMSOFT.7.103","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.7.103","url":null,"abstract":"The capability to propose feasible ways of binding a putative ligand inhibitor to a known receptor site is crucial to the successful structure-based drug design. A computer docking approach is to position or “dock\" ligand and receptor molecules together in many different ways and then score each orientation by applying a reasonable evaluation function. AutoDock3.0 is an unbiased type docking program in which a user does not have to direct a ligand to an active site, but the system finds an optimal position after a ligand is placed in a random manner. Synthesized derivatives of the intact inhibitor (inh1) of HIV protease were investigated for their docking modes as compared with their Ki values. Among the derivatives, inh3trans and inh6H were found to be more powerful inhibitors of HIV protease than the others. Gibbs free energy calculated by applying molecular mechanics interaction energies was compared with the one obtained by using experimental inhibitory potencies for a series of HIV protease inhibitors, and a fairly good correlation was found between the two. Based on this favorable correlationship between the computational and the experimental results, the computational experiments were pursued for the compounds drawn by Sybyl taking into consideration the fact that unexploited carbon affinity regions (or hydrophobic regions) with sizable volume were detected on the docking study of inh1 and inh8 against HIV protease. Those were compounds with a t-butyl substituted by various hydrophobic side chains. Among those a compound with a benzyl group exhibited the lowest docking energy. Since one of the goals of this paper was to perform the computational drug-design experiment to investigate potential HIV protease inhibitors, the authors would like to leave the clinical investigational work for the expertise of those areas.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115548194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2001-06-30DOI: 10.14827/JCCJ1999.13.105
M. Fukuda
{"title":"Vibrational analysis of water clusters by quantum chemical methods","authors":"M. Fukuda","doi":"10.14827/JCCJ1999.13.105","DOIUrl":"https://doi.org/10.14827/JCCJ1999.13.105","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"88 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131382193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Interactive Animation to Facilitate Understanding of the Visual Characteristics of Atomic Orbital Wavefunctions","authors":"S. Tokita, Takao Sugiyama","doi":"10.2477/JCHEMSOFT.7.87","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.7.87","url":null,"abstract":"QTVR (QuickTime Virtual Reality) と呼ばれるソフトウェアを利用して，水素原子の原子軌道 19 種について対話型動画表示を実現させた．この動画表示が，量子化学の教育にどのように役立つか調査した．対話型動画の利用は，軌道の形状と数式の関係，節の形状と数式の関係を理解する手助けとなることがわかった．","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115191736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：