NAMD入门教程(一) - 百度文库

solvate ubq.psf ubq.pdb Ct 5 Co ubq_wb

ȴнVMD͵solvateubq.pdbubq.psfĵ׷һˮСͼδڿԼһεˮΧףͼ

Ct 5 ֪ͨȷĸ߳ÿ귽ѡǸԭӣȻ5AΪ÷ı߽硣ע⣺ɵˮ岢һ塣߳ȡ󣨾ԭԶԭӵλáһ Co ubq_wbΪ֪ͨɵļнǵõļubq_wb.psf ubq_wb.pdb

2VMD TkConsole룺 set everyone [atomselect top all] measure minmax $everyone

ʱصֵϵԭĵԶĵꡣҪģԼҲ

measure center $everyone

ʱصֵϵġֵԺ󻹻õ ֵͼ

ڿʼһ֮ǰҪɵļcommonĿ¼ԷʡWindowsԴҵ1-1-buildĿ¼Ctrlѡļubq.pdb, ubq.psf, ubq_ws.pdb, ubq_ws.psf, ubq_wb.pdb, ubq_ws.psfȻǿnamd-tutorial/commonĿ¼¡ ʾ ˴ɵˮʵϹСˡʵӦʱӦ֤ˮ㹻Էֹ˶ʱˮҲҪʹڱ߽ʱ׺ܸԪĵ׾ײڱ߽ϸ֪ʶġ ⣬ӦעʵӦʱӦˮзӡرǵʵľɲΪ0ʱӦ趨ĿʹϵԵġڷʱӦǷϵоܵ͵㣬Խʡʱ䡣Ϊܻ͵Է˶ 2.3 ״ˮзأUbiquitinķӶѧģ

һУǽҪ״ˮķطӽ򵥵Ķѧģ⡣ ȣҪеķӶѧģĿʲôǽط״ˮУˮΧգȻNAMD趨õ¶ֵBoltzmann-Maxwell

ʷֲԭӸһijʼٶȣҪţѧ̣ˮԼиԭӵ˶켣ǵõĽģⷺһСҺ״̬µ˶״̬

֪ʶӣСƽ⣨Minimization and Equilibration ζѧģʵʰ̣Сƽ⣨Minimization and EquilibrationСʱNAMD趨ԭӵٶΪ0Ȼ󲻶ϸıԭӵλòϵܵ㣬ΪӶѧģijʼ״̬һDz¼ԭ˶켣ġΪԭӵλøıֻΪNAMDҪ״̬ʵ໥˶ ƽõʺˮ趨õĻ¶ȣԭӵٶȣ໥ãﵽƽ䣬ϵﵽȶ״̬شﵽֵ ΪʲôҪȽСΪṩϵпܰŤѹεļͼǡǽṹͬԴģʱĴṹкܸߵȽСֱӽƽ⣬ʻˮ໥ãָչ״̬ͷŵЩṹеĸһûġΪǴṹķӦǵҺеʵ״̬Ӷ˷˼ʱ䡣ˣͷľ˶໥տʹõʵΪҺеʵΪбҪƽ֮ǰΪ͵㣬ΪӶѧģijʼ״̬ һأӶѧģСƽ̡ͨǻȽʹ̶ˮ˶Сƽ⣻Ȼʺˮͬʱ˶ٴξСƽһѭһĿʹˮӴﵽСͨһܿĹ̡ȻٷſʣʹϵͳﵽСԼСֹһʼ׽ṹܲȶ һѾҪubq_ws.pdb ubq_ws.psf ļձ¿ʼᵽNAMDĸļ֪ҪļͿύNAMDжѧģˡļcommonļУǽȵõļ 2.3.1 ļ

ǰǰʹNAMDдţġšָļļ¼˽жѧģȫãNAMDֻҪõһļͿ԰Ӧָвڱζѧģ⣬namd-tutorial/1-2-sphere Ŀ¼¿ԵõѾԤϵļǽҪϸļݡ

дְ壬ڲ˵ѡ ļ򿪣ҵ1-2-sphere Ŀ¼ļѡȫ

ļͼȻļubq_ws_eq.confļܸӣǻϸÿһֵĺ塣

ע⣺ļУÿһпͷǡ#ݻᱻעͶԴNAMDеݡΪ˱֣#ļָɼ󲿷֡һǣ

############################################

## JOB DESCRIPTION ## ############################################ ˼һǶύ

1һ£Էļֳ¼֣ ? job description ? ɵ adjustable parameters ? ѧģsimulation parameters ? Ӳextra parameters ? ִнű execution script

ļ¼ĵʽṹļpdbpsfļλãļļԼѧģʱĻ¶ȣֹ㣬ȸֲڽжѧģʱֻҪṩNAMDһļNAMDͿҵļøֲҪжѧģ֮

2Ȼһ֣Job Descriptionһÿһпͷ#ֻע͡һļĿģMinimization and Equilibration of Ubiquitin in a Water Sphere൱һƬµĿ

3Adjustable Parameters һְ5 ? structure: õpsfļλ

? coordinatesõļpdbļλ

? set temperature 310: һtemperatureֵ310ԺҪʹ

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