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> Dear All,
> I am new to md and gromacs. According to the manual and some the 
> tutorial, one can set either temp coupling or pressure coupling or 
> both at the same time. Does the temp coupling alone mean to use NVT 
> ensemble and pressure alone NPT ensemble? What is it when use both 
> coupling?
> If I turned off pressure coupling in my md but temp coupling on, I got 
> about average pressure of -1000 bar. What does that mean? Is the 
> density of my system too high? If it is, how should I change it?
>
> Thanks for any input.

Hi,

First, NVT and NPT are well-defined ensembles, and not all 
pressure/temperature coupling methods reproduce them exactly. 
(Nose-Hoover for temperature and Parinello-Rahman for pressure).

"N" means constant number of particles.
"V" means constant volume (no pressure coupling) and "P" constant 
pressure (=coupling).
"T" means constant temperature and "E" constant energy (no temperature 
coupling).

Now, you might be tempted to always use the well-defined ensemble 
coupling methods, but that's not always a good solution. The methods 
above (often called "extended ensemble") lead to larger fluctuations 
and can sometimes oscillate. For instance, if you want to simulate at 
constant pressure it is usually better to first run a short simulation 
(say 100ps) with berendsen pressure scaling which is guaranteed to 
converge rapidly. Then you just turn off the pressure scaling and keep 
the box constant during the rest of the run.

Gromacs reports pressure in bar. A negative pressure means the box 
would like to contract, i.e. your density is slightly too low. Pressure 
will fluctuate a lot in a microscopic system (thousands of bars), so 
you can't tell anything until you have an average over a couple of 
picoseconds. Even then,  -1000 isn't horribly off for a condensed phase 
system - your density will probably only change by a couple of percent 
if you enable pressure coupling.

Actually - as soon as you enable pressure coupling there will be a term 
in the energy file for the density (measured in SI units = kg/m3).

Cheers,

Erik

Hi Erik,

  Along the same line, I have observed pretty large fluctuations in pressure
in my NVT + NPT simulation for 10ns. Below are some numbers:

Energy           Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------
Temperature      309.915    2.76174    2.76174 -4.33312e-07 -0.00216656
Pressure (bar)   1.00917      230.1      230.1 6.10213e-05   0.305106
Density (SI)     997.553    3.64684    3.64397 -0.000100151  -0.500756
Volume           70.0431   0.255603   0.255401 7.04046e-06  0.0352023

My reference T is 310K and my reference P is 1atm. However,
there's a fluctuation of +/- 230 around the desired average value of 1.0.
But density fluctuations are only around 0.3%.

Is this considered normal?
Or I should turn off pressure-coupling after say 1ns as what you suggested?


It is normal.

Thanks!

一个回复的例子(已接收)

Major comments:
1. The authors need to strengthen their results by including MMP
secretion, and tran-matrigel migration by a positive control
progenitor cell population i.e. enriched human CD34 cells
obtained from mobilized PBL, since this is a more clinically
relevant source of CD34 cells which has also been shown to
secrete both MMP-9 and MMP-2 (ref. 11). CD34 enriched cells
from steady state peripheral blood which also secrete MMPs are
also of interest.
2. In fig 1C please specify which cell line represents
MMP-negative cells. This needs to be clarified, as well as a
better explanation of the method of the protocol.
3. The ELISA results are represented as "fold increase" compared
to control. Instead, we suggest that standards should be used and
results should be presented as absolute concentrations and only
then can these results be compared to those of the zymography.
4. When discussing the results, the authors should distinguish
clearly between spontaneous migration vs chemotactic migration.
Furthermore, the high spontaneous migration obtained with cord
blood CD34 cells should be compared to mobilized PBL CD34
enriched cells and discussed.
5. The authors claim that the clonogenic assay was performed to
determine the optimum concentration for inhibition of MMP
activity by phenanthroline and anti MMP-9 mAb, however they
should clarify that this assay can only determine the toxicity of
the inhibitors and not their optimal inhibitory concentrations.

Minor comments:
1. There are many spelling and syntax errors, especially in the
results and discussion, which need correction.
a. Of special importance, is the percent inhibition of migration,
which is described as percent of migration. i.e. pg 7:"Migration
of CB CD34 was reduced to 73.3%?" Instead should read
"Migration of CB CD34 was reduced by 73.3%?"
b. The degree symbol needs to be added to the numbers in
Materials and methods.
2. It would be preferable to combine figure 1A and B, in order to
confirm the reliability of fig. 1B by a positive control
(HT1080).


Answer to referee 1 comment:
1. Mobilized peripheral blood is a more clinical source of CD34+ cells, so it is necessary to compare the MMP-9 secretion and trans-migration ability of CB CD34+ cells with that of mobilized PB CD34+ cells. However, we couldn't obtain enough mobilized PB to separate PB CD34+ cells and determine the MMP-9 secretion and migration ability, so we couldn’t complement the study on PB CD34+ cells in this paper. Results obtained by Janowska-Wieczorek et al found that mobilized CD34+ cells in peripheral blood express MMP-9. Furthermore, Domenech’s study showed that MMP-9 secretion is involved in G-CSF induced HPC mobilization. Their conclusions have been added in the discussion. In our present study, our central conclusion from our data is that freshly isolated CD34+ stem/progenitor cells obtained from CB produce MMP-9.

2. MMP-9 negative cell used in fig 1C was Jurkat cell. In zymographic analysis, MMP-9 was not detected in the medium conditioned by Jurkat cell. To exclude that the contaminating cells may play a role in the observed MMP-9 production, we screened the media conditioned by different proportion of CB mononuclear cells with MMP-9 negative cells by zymography. This result may be confusion. Actually, only by detecting the medium conditioned by 2X105 CB mononuclear cells (MNC)/ml (since the purities of CD34+ cell are more than 90%), it could exclude the MNC role. In the revised manuscript, we only detected MMP-9 activity and antigen level in the medium conditioned by 2X105 CB mononuclear cells (MNC)/ml. There is no MMP-9 secretion be detected in the medium conditioned by 2X105 CB MNC/ml. It excluded the possibility that the MMP-9 activity in CB CD34+ cells conditioned medium is due to the contamination by MNC.

3.In this revised paper, we have detected the MMP-9 antigen levels by using commercial specific ELISA kits (R&D System, sensitivity, 0.156ng/ml). Recombinant MMP-9 from R&D System was used as a standard. The results are expressed in the absolute concentration. The absolute concentration result has been added in the paper. As shown in Fig2, MMP-9 levels were detectable in both CB CD34+ cell conditioned medium and BM CD34+ cell conditioned medium. However, MMP-9 level was significantly higher in CB CD34+ cell conditioned medium than in BM CD34+ cell conditioned medium (0.406±0.133ng/ml versus 0.195±0.023ng/ml). Although gelatinolytic activity was not detected in media conditioned by CD34+ cells from BM, sensitivity of ELISA favors the detection of MMP-9 antigen in the BM CD34+.

4. In our study, to establish the direct link between MMP-9 and CB CD34+ cells migration, we only determined the role of MMP-9 in spontaneous migration of CB CD34+ cells, but not in chemotactic migration. Actually, regulation of hematopoietic stem cell migration, homing and anchorage of repopulation cells to the bone marrow involves a complex interplay between adhesion molecules, chemokines, cytokines and proteolytic enzymes. Results obtained by the groups of Voermans reveal that not only the spontaneous migration but also the SDF-1 induced migration of CB CD34+ cells is greatly increased in comparison to CD34+ cells from BM and peripheral blood.

5. CD34+ cells we obtained in each cord blood sample were very limited. It is not enough to screen the inhibitors concentrations to select the optimal inhibitory concentrations. In the blocking experiments, based on the concentrations used by others and the manufacturer's recommendation, we then determined the inhibitors concentrations by excluding the toxicity of the inhibitors in that concentration, which was determined by clonogenic assay.

Minor comments:
1.The spelling and syntax errors have been checked and corrected.
2.Since the results in figure 1A and B were obtained from two separated and parallel experiments, it is not fitness to combine two figures.

这是我的一篇修稿回复，杂志是JBMR-A,影响因子3.652,已发表，供参考！
Reply to the comments on JBMR-A-05-0172
Comment:
Reference #10 is missing from the Introduction but used much later in the manuscript. Should these be in order used in manuscript?

Reply:
The missing reference has been added into the revised manuscript.

Comment (continued):
What is the sample size for all tests performed?

Reply:
The sample size for drug release and PCL degradation tests was 3.0×3.0 cm2, with a thickness of about 0.1mm and a weight of about 40mg. This dada have been added into the revised manuscript.

Comment (continued):
Figure 7. There is no scientific evidence presented in the TEM figure to convince this reviewer of sub-jets. This statement on Page 9 cannot be made without clear evidence during the jet formation/separation. Figure 7 is just a large fiber and small fiber fused together, no other conclusion than this can be made.

Reply:
Necessary change in the statements has been made in the revised manuscript as well as in the referred figure accordingly.

Comment (continued):
Table 3: Need standard deviation for all values reported not just for a select few.. Equation after Table 3 not necessary. Just reference method used.

Reply:
Done accordingly.

Comment (continued):
Page 11: "faster weight loss" What was the sample size? Where is the statistical analysis of this data? This reviewer does not see a significant difference in any of the data presented, thus weight loss would be considered equivalent.

Reply:
Although not too much difference was seen, the conclusion that “the GS/PCL membrane exhibited a relatively faster weight loss compared with the RT/PCL membrane” was indeed applicable through “one-way analysis of variance (ANOVA)” analysis.
Following the reviewer’s comment, a new sub-section has been added to the manuscript to address the statistical analysis for the data.

Comment (continued):
Page 12: What is the sample size for release data? Looks like results based on a sample size of one? Need stand deviations on the data presented in Figure 11. Why wasn't release performed and compared for all electrospun conditions investigated otherwise?

Reply:
Three repeated tests were performed for each set of measurements and the resulting data were averaged. As stated in the revised manuscript, each sample had a square area of 33cm2 with a slightly different thickness.
Standard deviations have been added to the data shown in Fig. 11.
The present manuscript aimed to show that medical drugs can be encapsulated in ultrafine fibers through a co-axial electrospinning process. The drug release data intended to show that the encapsulation was successful. We did not consider any specific application in this preliminary paper, and in fact the two drugs were just chosen as model illustration. As such, there seemed not necessary to perform release experiments for all of the membranes electrospun with different conditions (i.e. the core concentrations)

Comment (continued):
Table 3: Yang's or Young's Modulus (page 10 says Young's).

Reply:
Corrected accordingly.

Comment (continued):
Figure 11: What is the % release, not just concentration. Why just this small sample of release data? Where is the release data for the other conditions?

Reply:
Unfortunately, we did not measure the amount of the shell material in obtaining the composite nanofibers. Namely, the flow rate of the shell solution during the electrospinning was not accurately controlled using an injecting pump. Hence the % release was not applicable.
Please refer to the previous reply related to Page 12 and Figure 11 for the remaining comments.

We acknowledge the reviewer’s comments and suggestions very much, which are valuable in improving the quality of our manuscript.

第一部分：选题与创新
一、先想先写最后做:
1. 做研究之前，必须想清楚：结果能不能发表？发表在哪里？
2. 先把文章大框写好，空出数据，等做完实验填完空就可以发了；正所谓心中有沟壑！
3. 在未搞清“写什么、发哪里、自己研究与同类研究有何出色之处”之前，就不要动手做！
4. 继续去看文献，去想；想不清楚就做还不如不做！
5. 要想这样做，就得先看文献！要知道如何把文章架起来、要知道别人是如何讨论的、要知道自己的数据是不是说明了与别人不同的东东或别人没有做过……这个过程就是阅读文献及思考的过程，这些搞清楚了，写就简单了！
6. 要是先做事，做完发现别人做过，或无法用理论来解释，岂不是冤大头？
二、如何科学选题:
　　1. 课题选择和国际接轨。想在国际核心期刊发表文献，就必须了解国际研究动态，选择与国际学术研究合拍的课题。由于多方面因素的影响，我国科学研究选题与国际先进水平还有一定距离。我国一家权威科研机构不久前在国内挑选了许多前沿领域的研究课题，准备参与国际合作，但到美国后发现近三分之二的课题已经不属前沿，在美国很少有人研究。在高校，一些教师治学严谨、基础扎实，但科研成果不突出，重要原因就是不重视有关领域学术动态，不能选得合适的课题。
　　2. 课题要有可发展性。课题可发展性对高水平论文的持续产出具有极大作用。中国科技大学范洪义另辟蹊径，发展了诺贝尔奖得主狄拉克(Dirac)奠定的量子论的符号法，系统地建立了“有序算符内的积分理论”，1998年有24篇论文被SCI收录；他对自己论文高产的解释是，研究“具有开创性，突破一点以后就可以向纵深发展，使研究工作自成系列、成面成片”。我院被SCI收录论文最多的杨新民老师从事凸性理论研究，该理论兴起于 20世纪70年代，90年代进入高峰。作为新兴研究领域，该理论本身有许多尚待研究之处，同时该理论也可用来解决最优化方面的问题。反之，有人由于所接触的问题已处于该研究分支的末端，即使在该点上有所突破，也难持续发展。
3. 借助工具选题：①查阅有关领域的检索工具，这些工具各高校都有；②了解SCI收录期刊所反映的科技动态，ISI期刊信息可从http://www.isinet.com查获，也可从SCI印刷版每期Ａ、Ｄ分册的来源出版物目录(Lists of Source Publications)查找，还可从ISI引用期刊报告 (Journal Citation Reports，简称JCR)了解期刊信息，该文献有印刷版、网络版(JCR on the Web)和光盘版 (JCR on CD-ROM)；③利用ISI提供的选题工具帮助，例如，能对正在开展的工作进行量化分析以保证用户科学研究同科学发展趋向一致的(Essential Science Indicators)，介绍有关最杰出人物研究状况、有关领域研究热点和发展趋向的(ISI Highly Cited.com)；④利用网上数据库了解国际学术研究动态及有关资料。只要有心参与国际学术竞争，选择与国际学术研究接轨的课题并不存在难以克服的障碍。
三、如何获得好的idea
无论是临床还是基础科研，最关键的是idea，idea的出台决定了科研水平和档次。高水平的科学家一听你的科研课题和方向，就能判断你科研水平。因此，获得好的idea是至关重要的。
1. 优秀科学家要具备敏锐的科研嗅觉，而这种敏锐性是经过长期的思考和实践获得的。通过几天或半个月的苦思苦想得到了一个自以为很好的idea，很可能是别人十几年前就做过的工作。但新手上路时重复一些经典实验以获得经验是很正常的。此外，科研要注重质量，千万不要为单纯地追求数量而令懂行的人嘲笑。如何获得idea呢？
A. 大量地、仔细地阅读文献，多听学术报告、多与同行探讨，从中获得启示，不能急于求成。
B. 总结感兴趣领域内尚未探讨过但很有意义的课题；
C. 总结争论性很强的问题，反复比较研究方法和结论，从中发现切入点；
D. 善于抓住科研过程中遇到的难以解释的问题，往往会成为思维的闪光点；
E. 细致地拟定方案，论证可行性。
2. 获得idea的两种途径：传统途径就是先阅读大量科研论文，弄清目前的研究现状和要解决的问题等；非传统的途径是自己先冥思苦想一段时间，有了自己的idea后再去查文献。这样不会让以往的研究限制你的思维，不失为一个很好的方法。别人没作过的东西，也许不是因为别人没想到，而是因为没有意义或者没有可能性。
3. 获得良好idea的基础前提：
A. 在科研前必须弥补基础知识，这是看懂文献的基础：《生物化学》《细胞生物学》《基因VIII》必看(先看中文版翟中和《细胞》王境岩《生化》赵寿元《遗传》朱玉贤《分子》；再看英文的Albez《cell》赖宁格《biochemistry》还有经典的《gene 8》)。
B. 广泛阅读文献是支撑。硕士至少查阅600篇，粗看300篇，细看100篇，研读50篇。博士至少再多一倍，并始终关注国际动态。《nature》《science》《cell》《PNAS》《JBC》《MBC》《Genes & Development》不放过，SCI-3分以上期刊应该耳熟能详！
C. 学会阅读文献，读懂文章。建议先review再article，先中后英；中文只看《科学通报》《中国科学》，其他不看；看10－20篇review后看研究性论文。拿到一篇研究性论文，先看标题，立即停住，问自己几个问题：(1)想想别人这文章是怎么做的(可参考材料方法)？会做哪些内容来说明其标题？(2)明白他为什么要做这个吗？(3)如文章是近半年内发表的，该文章解决了什么问题？引出了什么问题(结合你看的综述)？接下来仔细看摘要，就知道你的想法是否与别人吻合？(4)看完实验结果，再思考有什么地方不完善？有没有深入或拓展到底？一般来说，SCI-3分以下的文章只可能做了一部分机理，下面肯定有东西可做，关键是你自己要思考，去发现。
4. 长期作战持之以恒。做好上面所述要求肯定会有所谓idea，但过程艰辛，需长时间磨练，需要patience和passion。有天赋的人能考上海中科院生命科学院，北京中科院那几个所，北大、清华。耐心干5年，这些地方正为中国带来更多本土nature、science文章。
四、博士如何出牛文章？
1. 几点忠告：多看paper没有坏处；多找非老板的其他人，如其他教授，postdoc，前辈师兄等讨论，借鸡下蛋；可以动手的东西容易上手，比如软件等；找机会去开会，认认牛人，不发paper，做做volunteer，或者参加phd symposium之类。五主动参加seminar，自己讲几次看过的paper，最好自己组织一个topic拉几个师兄弟和postdoc参加，注意找几本教科书看看，打好基础。
2. 如何获得IDEA:
A. 需对研究的领域有一个全局性了解，按老板的话说是要有bird eye。
B. 要有bird eye，需比较全面地阅读本领域文章。读文章要其idea，总结成一句话，并用卡片记录好，分类整理。如果把别人文章的idea总结成一句话，就容易理解它的本质，也好作变化。
C. 读了很多文章后，可以写一个special study，将读过的本领域东西系统总结在一起，相当于你的综合理解，也就是bird eye看到的东西了。以后翻阅起来也相当方便。
D. 用心分析对于别人的idea，任何一个idea都有weakness；想办法解决它，那就成自己idea。最好的办法就是看大牛的paper，无论他有多牛，他的文章总是在说一个方面，总有其他东西没有包括进去，把他的文章认真精读了，总会发现漏洞和不足或不全面之处，然后你就知道怎么做了。记住：每篇文章几乎都有没有考虑完全的东西。
E. 时不时阅读更广泛领域的东西，扩大bird eye范围，对领域外的感兴趣的文章进行copy收藏，这个叫walk around a little bit，很多领域外的东西可以借鉴、学科交叉从而产生new idea。
F. 经常跟牛人、博士后或高年级博士等有思想的人(最好不是相同专业，而是相关专业或交叉学科)讨论，也容易出idea。再有就是，关注其他专业的书籍、杂志等信息，从中获取交叉创新idea

二部分：构思与撰文
一、写作框架和各部分要求
Title: Be short, accurate, and unambiguous; Give your paper a distinct personality; Begin with the subject of the study.
Introduction: What is known; What is unknown; Why we did this study?
Methods: Participants, subjects; Measurements; Outcomes and explanatory variables; Statistical methods.
Results: Sample characteristics; Univariate analyses; Bivariate analyses; Multivariate analyses.
Tables and figures: No more than six tables or figures; Use Table 1 for sample characteristics (no P values); Put most important findings in a figure.
Discussion: State what you found; Outline the strengths and limitations of the study; Discuss the relevance to current literature; Outline your implications with a clear "So what?" and "Where now?"
References: All citations must be accurate; Include only the most important, most rigorous, and most recent literature; Quote only published journal articles or books; Never quote "second hand"; Cite only 20-35 references.
Formatting: Include the title, author, page numbers, etc. in headers and footers; Start each section on a new page; Format titles and subtitles consistently; Comply with "Instructions to authors".
二、英文写作的语言技巧
1. Introduction：
A. 如何指出当前研究的不足并有目的地引导出自己研究的重要性？在叙述前人成果之后，用However来引导不足，提出一种新方法或新方向。如：However, little information(little attention/little work/little data/little research……)(or few studies/few investigations/few researchers/few attempts……)(or no/none of these studies……)has(have)been done on(focused on/attempted to/conducted/investigated/studied(with respect to))。如：Previous research (studies, records) has (have) failed to consider/ ignored/ misinterpreted/ neglected to/overestimated, underestimated/misleaded. thus, these previus results are inconclisive, misleading, unsatisfactory, questionable, controversial. Uncertainties (discrepancies) still exist……研究方法和方向与前人一样时，可通过以下方式强调自己工作：However, data is still scarce(rare, less accurate)or there is still dearth of……We need to(aim to, have to) provide more documents(data, records, studies, increase the dataset). Further studies are still necessary(essential)……
强调自己研究的重要性，一般还要在However之前介绍与自己研究问题相反或相关的问题。比如：(1)时间问题；(2)研究手段问题；(3)研究区域问题；(4)不确定性；(5)提出自己的假设来验证。如果你研究的问题在时间上比较新，你可大量提及时间较老问题的研究及重要性，然后(However)表明“对时间尺度比较新的问题研究不足”；如果你的是一种新的研究手段或研究方向，你可提出当前流行的方法及其物质性质，然后(However)说对你所研究的方向方法研究甚少；如果研究涉及区域问题，就先总结相邻区域或其它区域的研究，然后(However)强调这一区域的研究不足；虽然前人对某一问题研究很多，但目前有两种或更多种观点，这种uncertanties或ambiguities值得进一步澄清；如果自己的研究是全是新的，没有前人的工作可对比，你就可以自信地说“根据假设提出的过程，存在这种可能的结果，本文就是要证实这种结果”等等。We aim to test the feasibility (reliability) of the……It is hoped that the question will be resolved (fall away) with our proposed method (approach).
B. 提出自己的观点：We aim to//This paper reports on//This paper provides results//This paper extends the method//This paper focus on……The purpose of this paper is to……Furthermore, Moreover, In addition, we will also discuss……
C. 圈定自己的研究范围：introduction的另一个作用就是告诉读者(包括reviewer)，你文章的主要研究内容。如果处理不好，reviewer会提出严厉的建议，比如你没有考虑某种可能性，某种研究手段等。为减少这种争论，在前言的结尾就必须明确提出本文研究的范围：(1)时间尺度；(2) 研究区域等。如涉及较长的时序，你可明确提出本文只关心某一特定时间范围的问题，We preliminarily focus on the older (younger)……如有两种时间尺度 (long-term and short term)，你可说两者都重要，但是本文只涉及其中一种。研究区域的问题，和时间问题一样，也需明确提出你只关心某一特定区域！
D. 最后的原场：在前言的最后，还可以总结性地提出“这一研究对其它研究有什么帮助”；或者说further studies on……will be summarized in our next study (or elsewhere)。总之，其目的就是让读者把思路集中到你要讨论的问题上来。尽量减少不必要的争论(arguments)。
2. Discussion：
A. 怎样提出观点：在提出自己的观点时，采取什么样的策略很重要，不合适的句子通常会遭到reviewer置疑。(1)如果观点不是这篇文章最新提出的，通常要用We confirm that……(2)对于自己很自信的观点，可用We believe that……(3)通常，由数据推断出一定的结论，用Results indicate, infer, suggest, imply that……(4) 在极其特别时才可用We put forward(discover, observe)……"for the first time"来强调自己的创新……(5) 如果自己对所提出的观点不完全肯定，可用We tentatively put forward (interrprete this to…)Or The results may be due to (caused by) attributed to resulted from……Or This is probably a consequence of……It seems that……can account for (interpret) this……Or It is posible that it stem from……要注意这些结构要合理搭配。如果通篇是类型1)和5)，那这篇文章的意义就大打折扣。如果全是2)，肯定会遭到置疑。所以要仔细分析自己成果的创新性以及可信度。
B. 连接词与逻辑：写英文论文最常见的毛病是文章的逻辑不清楚，解决方法如下。
(1)注意句子上下连贯，不能让句子独立。常见的连接词有，However, also, in addition, consequently, afterwards, moreover, Furthermore, further, although, unlike, in contrast, Similarly, Unfortunately, alternatively, parallel results, In order to, despite, For example, Compared with, other results, thus, therefore……用好连接词能使文章层次清楚，意思明确。比如，叙述有时间顺序的事件或文献，最早的文献可用AA advocated it for the first time.接下来可用Then BB further demonstrated that. 再接下来，可用Afterwards, CC……如果还有，可用More recent studies by DD……如果叙述两种观点，要把它们截然分开AA  put forward that……In contrast, BB believe or Unlike AA, BB suggest or On the contrary (表明前面观点错误)，如果只表明两种观点对立，用in contrast BB……如果两种观点相近,可用AA suggest……Similarily, alternatively, BB……Or Also, BB or BB allso does……表示因果或者前后关系可用Consequently, therefore, as a result……表明递进关系可用furthermore, further, moreover, in addition……写完一段英文，最好首先检查是否较好地应用了这些连接词。
(2) 注意段落布局的整体逻辑：经常我们要叙述一个问题的几个方面。这种情况下，一定要注意逻辑结构。第一段要明确告诉读者你要讨论几个部份……Therefore, there are three aspects of this problem have to be addressed. The first question involves……The second problem relates to……The third aspect deals with……清晰地把观点逐层叙述。也可以直接用First, Second, Third, Finally……当然，Furthermore, in addition等可以用来补充说明。
(3) 讨论部份的整体结构：小标题是把问题分为几个片段的好方法。通常第一个片段指出文章最重要的数据或结果；补充说明部份放在最后一个片段。一定要明白，文章的读者分为多个档次；除了本专业的专业人士读懂以外，一定要想办法能让更多的外专业人读懂。所以可以把讨论部份分为两部份，一部份提出观点，另一部份详细介绍过程以及论述的依据。这样专业外的人士可以了解文章的主要观点，比较专业的讨论他可以把它当成黑箱子，而这一部份本专业人士可以进一步研究。
C.讨论部分包括什么内容？(1)主要数据及其特征的总结；(2)主要结论及与前人观点的对比；(3) 本文的不足。对第三点，一般作者看来不可取，但事实上给出文章的不足恰恰是保护自己文章的重要手段。如果刻意隐藏文章的漏洞，觉得别人看不出来，是非常不明智的。所谓不足，包括以下内容：(1)研究的问题有点片面，讨论时一定要说，It should be noted that this study has examined only……
We concentrate (focus) on only……We have to point out that we do not……Some limitations of this study are……(2)结论有些不足，The results do not imply……The results can not be used to determine(or be taken as evidence of)……Unfortunately, we can not determine this from this data……Our results are lack of……但指出这些不足之后，一定要马上再次加强本文的重要性以及可能采取的手段来解决这些不足，为别人或者自己的下一步研究打下伏笔。Not withstanding its limitation, this study does suggest……
However, these problems could be solved if we consider……Despite its preliminary character, this study can clearly indicate……用中文来说这是左右逢源，把审稿人想到的问题提前给一个交代，同时表明你已经在思考这些问题，但是由于文章长度，试验进度或者试验手段的制约，暂时不能回答这些问题。但通过你的一些建议，这些问题在将来的研究中有可能实现。

第三部分：选刊与投稿
一、拟投期刊的选择:
　　(1)选用SCI收录期刊。目前SCI收录核心刊 3000种，加上增补期刊约 5600种。研究者可事先将SCI中自己感兴趣的期刊找出来备用。
　　(2)利用SCI收录期刊的影响引子(Impact Factor)来选择期刊。期刊的影响因子是该刊前2年发表的文献在当前的平均被引次数。《科学》、《自然》影响因子很高，SCI收录中国期刊影响因子都在1.00以下。期刊影响因子愈大，有用信息愈多。作者可根据期刊的影响因子排名决定投稿方向。
　　(3)利用学科带头人的影响或国际学术交流的条件，物色最了解中国学术研究、信任中国学者的那部分期刊投稿。SCI选用的期刊中约 1 / 3为美国期刊，因而要注意选美国期刊。
二、如何准备投稿？
选择适合刊物投稿：从杂志homepage下载Instruction for Author，按投稿要求，如投稿份数、论文体例、长度、图表、参考文献引法、配图说明(Figure legends)等，逐条遵循。Letter to editor-in-chief : ①声明文稿权转让；②未一稿多投，和在稿件未作出决定前不准备一稿多投；③所有列出作者均对文稿有确切贡献；④文稿内容真实，无作伪；⑤所有作者均已阅读文稿，且同意送稿；⑥通信作者地址、电话、Fax、e-mail；⑦通信作者签名。勿一稿多投。
Title page 的式样如下：

Peroxisome Proliferation-Activated Receptor-g Ligands Ameliorate Experimental Autoimmune Myocarditis

Zuyi Yuan, MD, PhD; Yan Liu, MD; Yu Liu, MD; Jijun Zhang, MD; Chiharu Kishimoto, MD, PhD*; Yanni Wang, MD; Aiqun Ma, MD, PhD; Zhiquan Liu, MD.
Department of Cardiovascular Medicine, First Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; *Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
First author's surname: Yuan
Running head: PPARg ligands ameliorate myocarditis

Supported by Natural Science Foundation of China (30170371)
Address correspondence to:
Zuyi Yuan, MD, PhD
Department of Cardiovascular Medicine, First Hospital of Xi'an Jiaotong University,
No.1 Jiankang Road, Xi'an, Shaanxi 710061, China
Tel: +86-29-532-4021 Fax: +86-29-5263190
E-mail: zuyiyuan@mail.xjtu.edu.cn
三、向国外生物医学期刊投稿需注意
A. 期刊选择：
英文生物医学期刊种类繁多，选择一本恰当的期刊并非一件易事，然而这是论文得以发表的一个重要环节。选择期刊应考虑的因素：论文主题是否在刊物征稿范围内？论文格式是否符合刊物要求？论文是否符合刊物的一贯口味？关于期刊的声望(prestige)问题：期刊学术水平高其声望就高；反之声望则低。生物医学工作者都希望科研成果发表在有声望的高质量生物医学期刊上。选择期刊的方法：如果论文主题在一个很窄的分支学科内，那么选择范围只能限制在几种刊物；如果论文信息交叉了几个研究领域，则可有许多种选择。无论是哪种情况，先列出一个简单拟选期刊表，然后逐一对进行比较筛选，作出最后抉择。

第四部分：修回与退稿
一、正确对待审稿意见和退稿:
国际核心刊物的审稿人大多是各领域权威学者，杂志出版社经常征询编委意见，选择最佳审稿队伍。审稿是无报酬的，审稿人的工作态度大多极其认真。因此，对审稿意见要十分尊重，对每一条批评和建议，都要认真分析，并据此修改论文。自己认为不正确的意见，要极其慎重和认真地回答，有理有据地与审稿人探讨。如何对待杂志拒文，是作者犯难的问题。这里必须分析被拒绝的理由。第一类拒绝是“完全的拒绝”，主编通常会表达个意见，对这类文章永远不愿再看到，再寄送这类文章是没有意义的；第二是文章包含某些有用数据和信息，主编拒绝是因数据或分析有严重缺陷，这类文章不妨先放一放，等找到更广泛的证据支持或有了更明晰的结论后，再将经过修改的“新”文章寄给同一杂志，主编通常会考虑重新受理该文。有审稿人抱怨，个别中国作者在论文被一家杂志拒绝后又原封不动地寄给另外一家杂志，而他们再次被邀请审稿并对此非常反感，论文理所当然地被拒绝。《宇宙物理学》(The，Astrophysical，Journal)的科学主编Thomas提出：“论文被一家杂志拒绝后不经修改，又寄给另一个杂志，这是很糟的错误。通常，审稿人做了很认真的工作指出论文的问题，并建议修改；如果作者忽视这些忠告，是对时间和努力的真正浪费；同时，寄一篇坏的文章，对作者的科学声望是严重的损害。”影响因子不同的刊物接受论文的标准和要求差别很大。如果被拒论文不是由于文稿中的错误，而是重要性或创新性不够，作者仔细考虑审稿人意见并认真修改文稿后，可以寄给影响因子较低的刊物。值得注意的是，审稿人由于知识限制和某种成见，甚至学术观点不同，判断错误并建议退稿常会发生。如何处理情况？最近某青年的论文被杂志拒绝，经反复讨论检验，判断审稿人是错误的；为了论文及时发表，我们建议作者礼貌和认真地回信给主编并指出审稿人的错误，要求主编将意见转给审稿人，然后撤回论文再做必要改进，改寄影响因子更高的杂志；结果论文立即接受，并得到很好评价。另篇论文在某重要杂志经两年半才得以发表，主要原因是第一位审稿人对我国向量磁场测量的可靠性提出质疑，不同意发表。通过向权威同事请教和反复思考，我们确认所进行的研究及所采用测量都充分准确可靠；作者花了近两年时间与审稿人讨论，不但论文得以发表，还与审稿者和主编建立了良好关系，论文发表后得到良好的国际引述。
二、投稿后若干事宜：
(1)稿件追踪(follow-up correspondence)。如果投稿2周仍无任何有关稿件收到的信息，也可打电话、发e－mail或写信给编辑部核实稿件是否收到。
(2)稿件退修(revised manuscript)。几乎所有的经审查学术水平达到出版要求的自由来稿，在发表前都需要退给作者修改其表述及编辑格式，如压缩文章篇幅、重新设计表格、改善插图质量、限制不规则缩写词使用等。然而退给作者修改的稿件并不代表文章已经被接受，文章最终接受与否取决于作者对文章关键性重要内容和表述方式的修改能否达到审稿专家及编辑的要求。
通常退给作者修改的材料包括原稿、审稿专家意见、(reviewers' comments)和一封编辑的信(covering letter)。当作者收倒退修稿后，首先应该仔细地阅读退修信(modify letter)和审稿专家意见。然后应考虑能否或愿意接受审稿专家或编辑的意见，修改稿件。
(3)如何处理稿件修回？从主编回信和审稿人(reviewer)修回意见可看出文章录用的可能性。主编的回信会特别提到你文章的科学先进性(scientific priority)；审稿人对文章总的评价中会提到对文章是否感兴趣(interesting)等；修回不要仓促，反复阅读、理解审稿人的问题。对每位审稿人提出的意见要逐条回答(response to reviewer1，2，3)；对修回稿中已修改的地方要具体标明(page, lines)；给主编回信，感谢给文稿提出的修改意见，并指出按修改建议已作的修改，未作修改的地方要说明理由。

第五部分：其他内容
一、认识SCI论文
罗伯特•戴在其名著《如何撰写和发表科学论文》的序言中指出，“对一个科学家的评价，从研究生开始，就主要不是看他在实验室操作的机敏，不是看他对或宽或窄的研究领域固有的知识，更不是看他的智能和魅力，而是看他的著述。他们因此而出名，或依然默默无闻”。
A. 原创性和显著性是论文的生命:
在《再论科学道德问题》中指出，国际核心刊物发表的论文，原则上都应当是“在国际上首次”描述的新的观测和实验事实，首次提出的概念和模型，首次建立的方程，也包括对已有的重大观测(实验)事实的新的概括和新的规律的提炼。与原创性相联系，任何期刊都不希望发表已见于其它杂志，或由其它语言发表、或以稍有不同的形式发表的论文。太阳物理学权威刊物《太空物理学》(Solar，physics)主编Harvey专门谈到，少数作者主要结果用中文发表后又寄给《太空物理学》，这在过去是可以容忍的，但现在不允许。公认的原则是：作者不能把已在经过审稿的杂志发表的主要结果以不同形式投寄给其它杂志再发表。国际核心刊物的论文，不仅应该是原创的，其结果还必须是显著的，并对学科发展有所推动。用Harvey的话来说，“至少有一两个其他研究者会读这篇文章，并利用这些结果发表他们自己的工作。”对成果显著性的检验是论文被引用的多寡。作者应当关心自己论文被引用的情况，注意国际学术界对自己工作的评价，包括肯定和批评的方面，特别是注意同行们对自己发表结果的不同的理解；这是提高自己研究水平的重要途径。
B. 充分评价已有工作，体现作者学术水平:
是否客观而充分地评价了以往的工作，常常是审稿人和读者衡量作者学术水准和学术风范的重要方面。部分作者引述国外知名学者的工作，往往有点“言必称希腊”的味道，而对国内同行发表的工作重视不够。有时明明是中国学者首先做的工作，却没有得到自己国内同行的充分评价。应当提倡较多并适当地援引国内同行工作。但也不要学习少数日本作者，他们绝少引用日本学者之外的文章。部分同行在论文中引述相当数量公式，但却不列出公式的出处，让读者分不清是作者发展的，还是引自他人以往的工作。原则上：除了教科书上公认的方程和表达式外，对用于特定目的、特定条件和问题的推演，只要不是自己的工作，都要列出出处和适用条件；即便是作者以往的工作，也要列出相应文献，让读者在充分评价作者以往工作的基础上作必要参考，并清晰指出自己当前工作中独创性的贡献。这是作者对科学负责的表现，是一篇好的学术论文开宗明义必须写清楚的内容。
C. 特别重视论文题目、摘要、图表和结论:
每位作者都有阅读大量论文的经验。读者阅读论文的习惯一般是先浏览目录，对题目有兴趣才愿翻到有关论文；题目有兴趣的论文，读者又先读论文摘要；如果对摘要还有兴趣，接着会去看论文图表，因为图表往往最清楚地反映了论文结果。看过图表之后，如还有兴趣，会读论文的结论。通常只有少数读者会读论文的全文。作者应当清晰地知道，论文的题目将被数以千计的读者读到。对题目的每一个字都要审慎地选择，用最少的词语最确切反映论文的内容。
D. 花大力气提高英语写作水平:
英语不是我们的母语。我国SCI论文和引述偏少，除了基础研究水平的限制，语言的障碍不容忽视。每一位基础研究工作者必须把提高英语写作能力作为一个艰巨的任务。中国科技大学胡友秋教授总是把审稿人的英文修改和自己的原稿中被修改的部分单独抄在本子上一一对照，细心琢磨并背下来，一点一滴地提高英语写作水平；他寄往国际核心刊物的论文常被审稿人称为well-written。美国国家太阳天文台有一个内部审稿制度，目的是保证论文的正确性，对研究也有相互影响和砥砺的好处；未经内部审稿的论文不能寄给杂志。资深太阳物理学家Sara，Martin建议找一些可作为范例的论文精读，学习怎样组织和写出好英语；她特别提到已故著名天体物理学家Zwaan的论文可作范文。论文初稿完后定要检查拼写，避免简单的拼写错误；对英文写作无把握者，请英文好的同事或国外同行把把英文关是必要的。为从根本上提高英语水平，建议对研究生开设英语写作课程。

科技论文的写作要点

总体原则（3C）：Correct (正确)，Clear (清楚)；Concise (简洁)。

1 论文题名
1.1 基本要求 (1) 准确 (Accuracy)。题名要准确地反映论文的内容。作为论文的“标签”，题名既不能过于空泛和一般化，也不宜过于烦琐，使人得不出鲜明的印象。如果题名中无吸引读者的信息，或写得不堪理解。为确保题名的含义准确，应尽量避免使用非定量的、含义不明的词，如"rapid"，"new"等；并力求用词具有专指性，如"a vanadium-iron alloy"明显优于"a magnetic alloy"。(2) 简洁 (Brevity)。题名需用词简短、明了，以最少的文字概括尽可能多的内容。题名最好不超过10 ~ 12个单词，或100个英文字符（含空格和标点），如若能用一行文字表达，就尽量不要用2 行（超过2行有可能会削弱读者的印象）。在内容层次很多的情况下，如果难以简短化，最好采用主、副题名相结合的方法，如：Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive CDNA hybridizations (Proc Natl Acad Sci USA, 2000, 97(18): 9834 ~ 9839). 其中的副题名起补充、阐明作用，可起到很好的效果。(3) 清楚(Clarity)。题名要清晰地反映文章的具体内容和特色, 明确表明研究工作的独到之处，力求简洁有效、重点突出。为表达直接、清楚，以便引起读者的注意，应尽可能地将表达核心内容的主题词放在题名开头。如The effectiveness of vaccination against in healthy, working adults (N Engl J Med， 1995, 333: 889-893)中，如果作者用关键词vaccination作为题名的开头，读者可能会误认为这是一篇方法性文章：How to vaccinate this population? 相反，用effectiveness作为题名中第一个主题词，就直接指明了研究问题：Is vaccination in this population effective? 题名中应慎重使用缩略语。尤其对于可有多个解释的缩略语，应严加限制，必要时应在括号中注明全称。对那些全称较长，缩写后已得到科技界公认的，才可使用。为方便二次检索，题名中应避免使用化学式、上下角标、特殊符号（数字符号、希腊字母等）、公式、不常用的专业术语和非英语词汇（包括拉丁语）等。

1.2 题名的句法结构 题名通常由名词性短语构成，如果出现动词，多为分词或动名词形式。由于陈述句易使题名具有判断式的语意，同时一般也显得不简洁，因此，大部分编辑和学者都认为题名不应由陈述句构成。由于题名比句子简短，并且无需主、谓、宾，因此词序就也变得尤为重要。特别是如果词语间的修饰关系使用不当，就会影响读者正确理解题名的真实含意。例如：Isolation of antigens from monkeys using complement-fixation techniques. 可使人误解为“猴子使用了补体结合技术”。应改为：Using complement-fixation techniques in isolation of antigens from monkeys.即“用补体结合技术从猴体分离抗体”。

2 摘要
2.1 基本要求 (1) 确保简洁而充分地表述论文的IMRD，适当强调研究中创新、重要之处(但不要使用评价性语言)；尽量包括论文中的主要论点和重要细节（重要的论证或数据）。(2) 使用短而简单的句子，表达要准确、简洁、清楚；注意表述的逻辑性，尽量使用指示性的词语来表达论文的不同部分（层次），如使用“We found that...”表示结果；使用“We suggest that...”表示讨论结果的含义等。(3) 应尽量避免引用文献、图表，用词应为潜在的读者所熟悉。若无法回避使用引文，应在引文出现的位置将引文的书目信息标注在方括号内；如确有需要（如避免多次重复较长的术语）使用非同行熟知的缩写，应在缩写符号第一次出现时给出其全称。(4) 为方便检索系统转录，应尽量避免使用化学结构式、数学表达式、角标和希腊文等特殊符号。
2.2 摘要写作的时态 摘要写作时所采用的时态应因情况而定，应力求表达自然、妥当。写作中可大致遵循以下原则：(1) 介绍背景资料时，如果句子的内容不受时间影响的普遍事实，应使用现在式；如果句子的内容为对某种研究趋势的概述，则使用现在完成式。(2) 在叙述研究目的或主要研究活动时，如果采用“论文导向”，多使用现在式（如：This paper presents...）; 如果采用“研究导向”，则使用过去式（如：This study investigated...）。(3) 概述实验程序、方法和主要结果时，通常用现在式。如：We describe a new molecular approach to analyzing ...(4) 叙述结论或建议时，可使用现在式、臆测动词或may, should, could等助动词。We suggest that climate instability in the early part of the last interglacial may have...

2.3 摘要写作的人称和语态  由于主动语态的表达更为准确，且更易阅读，因而目前大多数期刊都提倡使用主动态，国际知名科技期刊 “Nature",“Cell"等尤其如此，其中第一人称和主动语态的使用十分普遍。

3 引言
3.1 基本要求 (1) 尽量准确、清楚且简洁地指出所探讨问题的本质和范围，对研究背景的阐述做到繁简适度。(2) 在背景介绍和问题的提出中，应引用“最相关”的文献以指引读者。要优先选择引用的文献包括相关研究中的经典、重要和最具说服力的文献，力戒刻意回避引用最重要的相关文献（甚至是对作者研究具某种“启示”性意义的文献），或者不恰当地大量引用作者本人的文献。(3) 采取适当的方式强调作者在本次研究中最重要的发现或贡献，让读者顺着逻辑的演进阅读论文。(4) 解释或定义专门术语或缩写词，以帮助编辑、审稿人和读者阅读稿件。(5) 适当地使用“I”，“We”或“Our”，以明确地指示作者本人的工作，如：最好使用“We conducted this study to determine whether...”，而不使用“This study was conducted to determine whether...”。(6) 叙述前人工作的欠缺以强调自己研究的创新时，应慎重且留有余地。可采用类似如下的表达：To the author's knowledge...；There is little information available in literature about...；Until recently, there is some lack of knowledge about...等等。

Hi Keith,

Reference frame and reference structure are references to the same
reference. It is the structure supplied with -s, and possibly a subset
of the atoms in there, specified by an index group. The RMSF is indeed
the standard deviation of the atomic displacement. That is an atom or
residue based property defined over a certain time, which is recorded
in the file specified with -o. The RMSD (-od [rmsdev.xvg]) is a
structure based property, defined over a range of atoms per time,
which is recorded for each frame in the trajectory. Thso the -o file
is indexed per atom (or per residue with -res) and the -od file is
indexed per time. Hence the differences between the numbers of
entries. That has nothing to do with the reference.

How may I check when a system reached it's equilibrium?

See if your protein folds and unfold many times.
But really, it depends on your system.

> This is a nontrivial question, and the answer partly depends on what you
> are trying to do. As David points out, if you want to do protein folding,

> say, your protein needs to have long enough to forget about its starting
> state (hence his comment about folding and unfolding). Usually that takes a
> prohibitively long time, though, for large proteins. So assuming you don't
> want to solve the protein folding problem you have to be content with
> something less. Definitely you want to run long enough that the protein RMSD > quits increasing, temperature and energy begin fluctuating around some
> relatively stable value,  and so on. You can also look for things like
> number of protein-water hydrogen bonds if you have explicit solvent; this
> tends to take a much longer time to equilibrate.
>
> Probably a good suggestion is to find out what other people have done who
> are doing something similar to you, and make sure you equilibrate at least
> as much as they do. :)

Hi Tamas,
just a remark about the rmsd with respect to the Xray structure: you
might want to plot rmsd vs log(time), that is a better check sometimes.
Cheers,
Lars

well, rmsd is not that bad. Just that it is easier to judge a converged
rmsd from a non-converged one when you plot it against log(t) instead of t.
Another convergence check is the cosine content of the traj projected
onto some (slow) PCA modes.
Cheers,
Lars

2. I just follow the steps in manual, but I am not
> sure if I reach to the real equilibrium state finally.
> How to check it? This is the most important thing for
> me now.
energy and other properties, e.g. RMSD, should converge to an
"equilibrium" value

> Hi
> As both the basic and acidic amino acid will be different protonation
> state at different pH environment, the pH will greatly affect the
> structure and function of protein. while the positions of hydrogen is
> hard to be earned using X-ray diffraction method, Is there a way to
> built protein models at different pH environment basing on a X-ray
> diffraction structure?
> Maybe a soft will do, does somebody know it, please give some advice,.

>
> thank you in advice
>
> zhou jinming

Hello,

Unfortunately there's no simple solution to this. An initial model can
be built by setting the protonation states according to the pH - you can
do it using pdb2gmx (in Gromacs). Then, you need to refine your model by
energy minimization. If you want to run an MD simulation, that might be
enough. However, if the pH that you need to work with is much smaller or
larger than the pH in which the protein was crystallised, the protein
may be deformed, and you may need to equilibrate it for a long time
before you get any meaningful model.

Ran.

Hi,

There is a method in the Amber package to run MD at constant pH,
where the protonation states of the amino acids are varied by an MC
method. I have never used it and don't work in this area myself, but
it's something to be aware of if you're starting a project.

Dave

> I still have another question of "gen_vel".
> Does "gen_vel=yes" or "gen_vel=no" influence the mdrun result much?
> Or what kind of properties will be greatly changed as "gen_vel" option
> changed?

Setting gen_vel = yes will generate velocities, which will speed up
equilibration (very) slightly.

Thank you very much for your kindly help, Xavier, David,
Having read your comments on gen_vel and tpbconv, I want to put my 
understanding here.
Please check if they are correct
normally,
1. "gen_vel=yes" with "gen_temp=ref_t" (ref_t for T-coupling) will speed up 
equilibration slightly.
2. for a new simulation, "gen_vel=yes" should be set for PR-MD, and 
"gen_vel=no" for the final MD, velocities at t=0 will be read from the gro 
file;
for a continuation md simulation, "gen_vel=no" should be set, otherwise you 
start a new simulation from the structure or conformation of the previous 
simulation.
3. to continue a complete run, just using the final gro and "gen_vel=no"; or 
use tpbconv with -until or -extend option.
4. to continue a crashed run with tpbconv, gen_vel does not influence 
because velocity will be read from trr file.
to continue a crashed run, with T, P coupling
set in mdp file, eg. "nstxout=10000" and "nstvout=10000"
# check the last complete frame containing
gmxcheck_s -f md.trr
# dump the last frame with higher precision
trjconv -f md.trr -s b4md.tpr -n index.ndx -o frame.gro -ndec 6 -dump 1234
#  convert the dumped frame back to trr format
trjconv -f frame.gro -n index.ndx -o frame.trr
#  generate new tpr file with restart coordinates & velocities
tpbconv -f frame.trr -s b4md.tpr -n index -e md_ener.edr -o restart.tpr
#  Re-start with the new tpr file
mdrun -s restart.tpr -o md2.trr ...

linux应用软件谈之远程桌面控制篇

这里我要说的不是telnet,rsh之类的远程控制工具,而是指远程控制桌面应用.
　　
　　　　X window比MS windows先进的地方是,X window是个基于网络的的图形视窗系统,本身就具有远程控制的强大功能.用户在远程系统上登录执行X 应用程序,并将Xclients执行的结果传回本地主机.这就是我下面要介绍的Remote X
　　
　　　　一、Remote X
　　
　　　　假设本地主机ip为172.16.1.1,远程的主机ip为172.16.1.2
　　
　　　　第一步,在本地主机上的任意一个xterm中执行xhost,用来允许远程的其它主机可以和本地主机的X server联网:
　　
　　xhost + 172.16.1.2
　　
　　　　如果不指定任何ip地址,则表示权限完全放开,这会带来安全问题,要小心!
　　
　　　　第二步,确认本地主机的xfs是运行的.用ps检查一下进程.
　　
　　　　第三步,从本地主机(172.16.1.1)上通过网络登录到远程主机172.16.1.2上,你用telnet,ssh,rsh都可以.设置DISPLAY变量.
　　
　　export DISPLAY=172.16.1.1:0
　　
　　　　第四步,现在可以使用远程主机上的X 应用程序了.
　　
　　　　这么样,很方便吧,但是你还不能掌控整个桌面环境,这个工作就交给vnc吧!Remote X 在局域网上运行效果很不错,普通的电话拨号就不用试了,速度太慢了.
　　
　　　　二、vnc
　　
　　　　我相信有不少人在windows环境用过pcanywhere,但你想不想用一个免费的,可以在linux,win9x/nt上都可以使用的pcanywhere,这就是vnc.
　　
　　　　vnc就是vitual network computing的缩写,它支持许多操作平台,甚至可在浏览器中操作.
　　
　　　　我主要介绍vncviewer的用法,以及用linux远程控制linux或nt.
　　
　　　　vnc client通过架构在tcp/ip上的vnc协议与vnc server沟通,通过认证后,把X server的桌面环境,输入设备,和X 资源交给vncserver掌控,vnc server将桌面环境通过vnc 协议送给vnc client端.让vnc client来操纵vnc server桌面环境和输入设备.
　　
　　　　首先下载到vnc的linux版本和windows版本.
　　
　　　　当前的linux版本是vnc-3.3.3r1_x86_linux_2.0.tgz
　　
　　　　当前的windows版本是vnc-3.3.3r7_x86_win32.zip
　　
　　　　1.安装linux版的vnc
　　
　　　　(1)安装
　　
　　tar zxvf vnc-3.3.3r1_x86_linux_2.0.tgz
　　cd vnc_x86_linux_2.0
　　cp *vnc* /usr/local/bin/
　　mkdir /usr/local/vnc
　　cp -r classes/ /usr/local/vnc/
　　
　　　(2)设置vnc server的访问密码
　　
　　vncpasswd
　　
　　　　(3)启动vnc server
　　
　　vncserver
　　
　　　　注意运行后显示的信息,记下所用的端口号,一般从1开始,因为0被x server占用了.现在,你就能提供vnc服务了.vnc client的用法等会介绍.
　　
　　　　2、安装nt版的vnc
　　
　　　　1)安装
　　
　　　　解开vnc-3.3.3r7_x86_win32.zip包后,会产生winvnc和vncviewer两个目录.winvnc目录中是vnc server的安装程序,vncviewer目录中是vnc client的安装序.我只关心vnc server,在winvnc目录中执行setup即可.
　　
　　　　2)设置
　　
　　　　首先执行install default registry settings.
　　
　　　　run winvnc(app mode)就是执行vnc server
　　
　　　　这时可看到winvnc运行的小图标,用鼠标右键点击图标,在properties/incoming connections中设定密码.默认配置即可.
　　
　　　　现在,你的nt就能提供vnc服务了.
　　
　　　　3、使用vncviewer
　　
　　　　vnc server启动成功后,你就可用vncviewer来远程控制桌面了.
　　
　　vncviewer xxx.xxx.xxx.xxx:display number
　　
　　　　例如,vncviewer 172.16.1.2:1
　　
　　　　按要求输入密码就可以看到远程的桌面了.
　　
　　　　注意:viewers需要在16位色的显示模式下工作，如果您的操作系统中没上16位色，那么请您及时的调整您计算机的显示模式。不然vncviewer无法正常工作。
　　
　　　　4、linux版vnc server的改进.
　　
　　　　linux上的vnc server内定的桌面管理环境是twm,实在是太简陋了.
　　
　　　　修改＄HOME/.vnc/xstartup这个文件.
　　
　　　　把所有内容的行前加上#,再在接尾部份加上:
　　
　　startkde &
　　
　　　　你当然可用你喜好的桌面代替.我这是用kde来代替twm,速度会慢少少,但用起来方便不少.
　　
　　　　注意要重新启动vnc server.
　　
　　　　5、通过浏览器使用vnc
　　
　　　　通过浏览器使用vnc,要注意端口号的变化.
　　
　　　　假设vnc server是172.16.1.2:1的话,那么,可用浏览器访问http://172.16.1.2:5801
　　
　　　　端口号=display number + 5800
　　
　　　　好了,心动不如行动,just do it !