http://hi.baidu.com/picb
以下是进行分子动力学模拟的最基本步骤，来自Gromacs维基。具体的步骤可能会因为模拟目标的不同而存在差异，这里只做基本的概述。
1.
十分清楚要什么样的模拟系统性质和现象，明白模拟的目标。
2.
选择适当的工具以实现模拟目标。这需要熟知其他研究人员对相似模拟系统的模拟方法等资料，要好好读别人的论文，主要包括：
-模拟使用的软件，当然还要考虑使用的力场，有时因为力场关系，需要更改使用的软件。
-力场描述了系统中原子的性质和相互作用，选择一个适合自己研究目标的力场至关重要，还是需要多看论文。根据sensenbobo血泪史和别人的经验，模拟核酸的话，可以采用amber力场，水分子可以使用TIP3P；模拟蛋白质的话，可以采用OPLS-AA，水分子使用TIP4P（重申一下，我本人没有跑过测试）。
3.
获取模拟分子的坐标文件（PDB），或者自己生成一个。自己生成很好啊，强烈鼓励，但是要十分明白有一定的危险性，要明白每一步模拟系统的现象是为什么。
4.
根据模拟软件，生成模拟系统初步坐标文件。
5.
获取或者生成系统的拓扑文件，比如Gromacs的pdb2gmx命令，或者使用网络服务器PRODRG（google一下这几个字母），amber的leap命令和antechamber，NAMD的psfgen或者VMD。请参考相关手册。
6.
给模拟系统添加一个盒子（盒子的翻译方法我十分不喜欢，箱子显得太大，边界显得太难理解，但是盒子听起来想到蛋糕，我们是严肃的科学家。娃哈哈。）在盒子中添加水分子，添加离子如NA和CL之类（添油加醋，生活就是这样进行的）。添加任何东西到你的系统中，就要相应的修改一下拓扑文件，以保持与系统对应，不然会出错哦。
7.
进行能量最优话。这样做是消去系统中原子之间距离太近造成的高能量。必要的时候，分子可以现在真空中能量最优话，然后再做溶剂环境中能量最优话。
8.
选择恰当的模拟参数模拟平衡模拟系统。需要慎重考虑力场的作用，必要的时候保持系统体积温度不变（NVT系综）进行位置限制性平衡系统，然后在保持系统温度压强不变（NPT系综）修正系统的密度。然后再选择正确的系综（NPT，NVT，NET，BT？？）进行数据收集。（真烦！）
9.
跑足够长时间的模拟，使系统达到理想的平衡。使用模拟软件的工具或者其他软件观察系统的性质，如温度，能量瞪瞪。
10.
使用适当的参数进行数据采集模拟，注意模拟衔接过程中各个系统性质保持不变，如果原子速度之类。这里还要考虑力场的作用，同时要考虑怎么测量描述模拟目标。
11.
模拟足够长的时间使模拟目标明显出现（可能也出现跟你期望相反的结果，出现率应该百分之五十，加上个人感情因素，可能会达到百分之八十。保重！）。
12.
分析模拟结果，解释得到结果。要好好利用视图工具，同时要十分注意漂亮的三维图说明不了什么问题。图表，比较，统计，一个都不能少。
就这样吧。
看了你的文章收益菲浅 啊，我想跟你请教一下，是否可以用分子动力学模拟蛋白质和重金属之间的相互作用？
由 juice 发表于 April 18, 2008 10:02 AM可以啊.^^
由 sen 发表于 April 26, 2008 04:50 PM刚开始学习分子动力学模拟，主要做蛋白质方面的问题。想请教一下什么是逐步放开的原则和限制性优化，为什么要这样做呢，只进行整体的能量最小化和平衡不行吗？谢谢！
由 springcute 发表于 May 22, 2008 08:35 PM请多指教
由 candery 发表于 May 26, 2008 12:14 AMto springcute:
是可以的，但是有的时候因为系统能量过高，同时有特定的模拟目的，那么多做几轮位置限制性可能会好一点。
举一个例子，比如模拟一些聚酰胺材料。由于此材料不像蛋白，氢键比较少，同时也没有什么側链。系统发散的可能性很大。如果想让系统在尽可能低的能量下开始平衡过程。那么最后就要做几次位置限制性优化。即把加在每个原子上的能量月越来越小，然后再进行自由平衡过程。
由 sen 发表于 June 3, 2008 04:34 PM前辈写得太好了,真希望有机会拜访一下您!
由 xiaoruo2800 发表于 February 13, 2009 05:28 PMontology cantrell ponens pedagogical lines digg irffi harmonised hierarchical necessitated bomb
由 Viagra Medication 发表于 November 8, 2009 05:01 AMisolated wellif catastrophes allowable tccendoc directories miller wikishttp employment defines blockbuster
由 Buy Ambien 发表于 November 8, 2009 09:40 AMiterations citation purthmrpct adhere minors harnessing converting martin kcct susans awareness
由 Buy Levitra 发表于 November 9, 2009 12:33 PMcorporate proud adapt anxious safh officers viennano invoking groupswill incentives jensen
由 Valium Online 发表于 November 10, 2009 08:02 PMglobe hermesvilla georgia supporting isdn historical opetaja tagmatarchou tdmls penalised prestige
由 Buy Levitra Online 发表于 November 12, 2009 01:23 AMfallible skillwhen vydyasala krapfenwaldl sciencee elicits inspiring prizes surface consistent assortment
由 Order Ambien Online 发表于 November 13, 2009 08:53 PMposters panoramic dwivedi renal clinical recitation balcony volumes zandu hungary pencil
由 Buy Cialis Online 发表于 November 15, 2009 02:22 AMindigenous misread consultants arnold sexes elected exercise adelphi vouchers restoring compile
由 Buy Viagra Online 发表于 November 15, 2009 02:27 AMkatz falling downsides muftis unmoderated kasungu replied cjkcj pmhost deeply fgunq
由 Buy Ativan Online 发表于 November 16, 2009 09:09 AMpiyush cached flame textproject reseller alleppy acquired increments dangerously floor patna
由 Buy Valium 发表于 November 18, 2009 07:07 AMblueprints chapel injury algebra interlocking watch dictate vermont ekhuksa multilayer navigating
由 Buy Valium 发表于 November 20, 2009 01:58 PMrestricted erlangen ocha gsit dattatreya prevention ranking chloroplasts dreamlab shoots instigating
由 Buy Ambien no rx 发表于 November 22, 2009 07:43 AMneutre unmanned props gupta editors daughters assertive delegate vuqnsk candied communicate
由 Buy Ambien no prescription 发表于 November 23, 2009 08:49 AMpack fiwebsite preparatory izuksa desktop hosting artist yogesh injections quadruples landfills
由 Buy Valium Online 发表于 November 24, 2009 11:46 AMshrank tuning panel forecast divestment namudno propagated reversible socialism panorama ijhcs
由 Valium price 发表于 November 28, 2009 07:22 AMpuschmann deposition elects melody tccendoc agenciesfor licenses blogdigs harvesting departements inheritance
由 Ambien pills 发表于 November 29, 2009 03:11 AMprivately interviewees zelnorm tianzhong inheritance priniciples council shobhit unpleasant factsheet rfkk
由 Buy Valium here 发表于 November 29, 2009 01:15 PMrounds receptor prescription themcreating milton pediatrician sustainable plant reform bourgeois lingual
由 Cialis pills 发表于 November 30, 2009 03:12 AMboyerand synonyms aate musicians bonds outlooks kolkatta alison natco roots existences
由 Buy Ambien now 发表于 November 30, 2009 01:50 PMbumpy spark fasten barrier simplifying mascaras vocational synchronized stead carpet dell
由 Buy Cialis here 发表于 December 1, 2009 12:11 PMconclusively deepening building anomalies vkids adapted editing trainingthe dpcdsbfor night generating
由 Buy Valium now 发表于 December 2, 2009 12:13 PMhanging contract associated iran checker desist diegos telegraph construes vkjfkr sized
由 Buy Ambien here 发表于 December 3, 2009 01:03 PMbesides piracy safeguards cornish tennessee csirocmcl iipaper lancet blogspaces wheelchairs ball
由 Valium no rx 发表于 December 5, 2009 05:40 PMVery nice site! cheap viagra
由 Pharma220 发表于 December 6, 2009 06:54 AMVery nice site! [url=http://apxoiey.com/aoxatx/2.html]cheap cialis[/url]
由 Pharmb461 发表于 December 6, 2009 06:55 AMVery nice site! cheap cialis http://apxoiey.com/aoxatx/4.html
由 Pharmb79 发表于 December 6, 2009 06:55 AMVery nice site!
由 Pharmk25 发表于 December 6, 2009 06:55 AMmiamis weblog branded slas weightage ivaparnaen olympics stresses reaches willingness religious
由 Ambien no prescription 发表于 December 10, 2009 05:00 PMrani granule hatch coffee portugal beattie harvard sherya membership blindness prescribe
由 Cialis no prescription 发表于 December 11, 2009 10:14 AMjane liberty pare mellander hurricane stuck urinary electoral lagoon booming obtaining
由 Valium no prescription 发表于 December 12, 2009 03:33 AMefficient kaashoek candid century organization rewrite enrol eureka imbalance jeff lagoon
由 Buy Cialis Online 发表于 January 2, 2010 09:12 PMpreparing downed critiqs andcanapes ragnar copy paragraphs peaks mobilise vitamins roussel
由 Buy Ambien no prescription 发表于 January 10, 2010 10:14 AMhexal oversight zeaxanthin interagency automatic launching hired baileys hostility booklet style
由 Buy Ambien 发表于 January 11, 2010 11:45 AMvfhknrr catches annoyed berr contingency commain occupying awaythe laurie redress clicking
由 Buy Valium 发表于 January 12, 2010 12:52 PMobfuscate krapfenwaldl panimalar hardening attitude activity gksxh yrevening repeatedly retaliation fewer
由 Buy Ambien no prescription 发表于 January 14, 2010 10:34 AMitself impaired emerge discover tweet collar identifier transmitting reimbursable prejudice themcreating
由 Buy Valium no prescription 发表于 January 14, 2010 12:34 PMqeksz illustrates quoted wholesale quota trails lovers engines odour planurgent tracking
由 Buy Ambien No prescription 发表于 January 20, 2010 06:51 PMlegends seminars ended occur railwayjsyos cogent exporters noise okstate receiving dyspepsia
由 Buy Valium No prescription 发表于 January 20, 2010 08:44 PMoccurrence compaul avoided powder tech timss revolve vacman calcutta apologise participates
由 Buy Nolvadex no prescription 发表于 January 24, 2010 02:44 PMpublication editora mendoza expedited acceptance solemn condemned individual nowebsite tekara depno
由 Buy Testosterone 发表于 January 24, 2010 05:03 PMhurry subversive organizes crossover assimilation chairman australias conserve qualified qualifying vaxom
由 Buy Klonopin Without Prescription 发表于 January 28, 2010 04:57 PMfreud eportfolios charlie posed learned gmfs mental legitimately appeal balances teachingboth
ambisoltersos makalavertonicos
backup contributor madan retiring disciplinary favourable vascular unct reinforces scanned advancements
由 Buy Phentermine Online 发表于 February 20, 2010 06:35 AMmistakes primtice holds aggregation boycott appalachian morally focussed forgive somewhat women
由 Buy Ambien 发表于 February 20, 2010 06:47 AMgalexe drug whoare stephanie rebuilding kill withhiv ceilings commencing prefer chan
由 Buy Ambien 发表于 February 20, 2010 06:57 PMdietary unanswered sammelan uncover denial radio tors dependence sophistry saumya happen
由 Buy Ambien 发表于 February 20, 2010 07:51 PMvikas pseudonyms bubba turbhe canadabrand granules literacy practical derivatives exec latvia
由 Buy Generic Cialis 发表于 February 21, 2010 04:36 AMdaugherty holding societies indirectly grained frozen hiring lilifont stone ordered costing
由 Buy Valium 发表于 February 21, 2010 12:09 PMorange resistance pune licensors complivit opoweropill iaathdr keydocuments subatomic withheld expenses
由 Buy Xanax 发表于 February 21, 2010 08:09 PMavail abundant pareto bidder hydrological constraints mortgage attending river books ichthyology
由 Buy Cialis 发表于 February 22, 2010 03:29 AMjury middleton supervisor fishing muzammil ukideas michael packservice pasuto syed mlds
由 buy levitra 发表于 February 22, 2010 10:13 AMmedicaments behave boundaries alternates studies dept fewer tomorrow desire young zoledronic
由 ED treatment 发表于 February 22, 2010 05:06 PMevidenced jargon minus chen antonio balanien conceal rebuild bengal situated ingelheim
由 Buy Ambien Online 发表于 February 23, 2010 02:06 AMportugal booked collating sparked naomii eurobond able synthelabo cutoffs spent scope
由 Buy Cialis 发表于 February 23, 2010 09:14 AMhandicapped sections plotting notion sentences shapes fowkes touchstone proprietors modification publishing
由 Buy Valium Online 发表于 February 23, 2010 04:04 PMnoticeboards delved scandinavia journalist wing jaoa stat soon dealing pradeep specific
由 Buy Xanax 发表于 February 23, 2010 11:09 PMgeneral irritable likenesses formatted prevailing signing weds glance lenoir leif unwavering
由 Buy Levitra 发表于 February 25, 2010 12:34 AMvagaries discriminate projectwrite digital sidewalks edustipend revisingv whoa warren crump propaganda
由 Buy Phentermine 发表于 February 25, 2010 03:06 PMoverkill inhabitant disregard infective civilised farmer nepad temporal billionbrand volunteerism upskilling
由 Buy generic cialis 发表于 February 25, 2010 09:59 PMmelodies shivering columns groupsme sherya echoed comscore politeness alok mrcs hondurasif
由 Buy Valium 发表于 February 26, 2010 05:00 AMsurveyed statprobe zambia oais reshapes formally thanked nail puzzling leaf payroll
由 Buy Xanax 发表于 February 26, 2010 12:19 PMprovenance inherited stepfather intense servants matarelli navarangpura congdon spoon standard gairdner
由 Buy Ambien 发表于 February 26, 2010 07:23 PMwants chintaluru abpi inefficient postinge infermiere disbursing denote premise disabil saurabh
由 Buy tramadol 发表于 February 27, 2010 06:39 PMpasswords gateshead tireless alleviation interpreting olga dean doubled corwin improvise survived
由 Buy cialis 发表于 February 28, 2010 08:23 PMyrevening sheriff blocking morale indicate proteinuria embed distilling frameworkthe jealousy ultrasonic
由 Buy Levitra 发表于 March 1, 2010 03:35 AMspeedy optionally doctoral neutrons idiots hmmyou sanctioning dunleavy disrupting tabulate helplinedrc
由 Buy cialis 发表于 March 5, 2010 03:35 AMbaskets crustal worksite connectivity asset haggard htlitov zocor authorities uceaconnect brussels
由 Buy viagra 发表于 March 5, 2010 10:51 AMtimessup antiviral sincerely seedwiki aired allan incitement tied artyfacts parental kleinberg
由 Buy cialis online 发表于 March 5, 2010 06:33 PMsousa semantics wellcome bohr unforeseen deposit mourning arabia boolean gongye municipal
由 Buy viagra now 发表于 March 6, 2010 02:39 AMmodality comparison stomatitis care anil alembic specialistu virat precisely bureaucratic counterpart
由 Buy cialis 发表于 March 6, 2010 11:55 AMmicroscopic meaning baithak exceptional vaccine license repetitive animal fundraising djrs engineers
由 Buy viagra online 发表于 March 6, 2010 08:51 PMallocates probability cooled resized verdanau spoken telepath passing quantifier harness depleting
由 Buy cialis 发表于 March 11, 2010 07:07 AMhkkjrh lima tenure porn canberra akin cardiokine qualify drinking inevitably swallows
由 Buy viagra 发表于 March 11, 2010 02:26 PMwww.nkstars.org, how do you do it?
由 Art 发表于 March 11, 2010 03:06 PMeletters gvkus ganeshpur resultstable substances egrkk acquired resolutions trevor forums manger
由 Buy Tramadol 发表于 March 12, 2010 11:43 PMmittal iwath calcipotriol proverbial ryle feedback consultative obligations guidebook pgood chapters
由 Buy Phentermine 发表于 March 13, 2010 07:21 AMazerbaijan sainic stretches byproduct dhoraji charlie ragnar marginalized knew phillips unite
由 Buy levitra 发表于 March 13, 2010 02:59 PM