VMD is a wonderful and powerful freeware and multiplatform software for… umh… almost everything thank to the possibility to use plugins and custom tcl scripts. At the moment, I use it mainly to display molecules, but stay tuned because big things will come (I have a student that will do… suspence!!!)
If you are interested in a collection of tcl scripts for VMD, go .
Table of Contents
VMD can be downloaded for free from the . You will need to create a free account in order to access to the download area. The last version is the 1.8.7 released in the beginning of 2009.
Take your time to read the
(very useful) and if you have troubles, you can also search the
or have a look at the .
Installation (Linux)
Once you have downloaded the source, uncompress the tarball in a temporary directory. Run the command
[user@desktop]$ ./configure LINUX
[user@desktop]$ ./configure LINUXAMD64
if you have want the 64bit version. This will produce a proper makefile. Now move in the src subdirectory and install VMD as:
[user@desktop]$ sudo make install
This will install vmd in the default directories.
VMD in 3 slides: a quick tour
Two and a half, to be honest. I wrote these slides as part of a hands-on workshop for students coming in the lab for short stages or practical courses.
The pdf can be downloaded . This is just a very basic and incomplete introduction: VMD is really a great piece of software and will not take longer for you to fall in love with it and to ditch your preferred scripting language for tcl scripting in VDM.
Step By Step Tutorial: VMD Basics
Explain a program so rich of functions as VMD is never easy. So I have thought, as experiment, to make a step by step tutorial in pdf to illustrate the basics of VMD. I will update and expand this tutorial in time. Here some images:
The tutorial in pdf can be downloaded , and redistributed as soon as you keep it freeware and do not remove the watermark linking to this site.
Work with VMD
Load/Save structures
Here a small introduction on how to load and save structures with VMD. The video tutorial will enter more into details.
Loading a single structure
VMD can load data saved in huge number of chemical formats: gromacs, tinker, charmm, amber, gamess, gaussian, vasp, pdb, xyz, and more. The fastest way to load a structure is to launch VMD providing the file to load, as in the example below:
[user@chembytes]$ vmd water.xyz
VMD will try to use the correct plugin guessing from the extension of the file to load, e.g. xyz. If the extension does not load the proper plugin, you can specify the format of the file. As example, let's consider a Tinker file: usually, the extension for such file is xyz, but the format is different from the standard cartesian XYZ. VMD will try to use the cartesian XYZ plugin and will fail opening the structure. You need then to specify the format of the file as in the example below:
[user@chembytes]$ vmd -tinker water.xyz
Structures can be loaded also from inside vmd, using the graphical interface, as explained in the slides provided in the previous session. Just go to File-&New molecule and load the file in the &Filename& field and, if needed, set the proper type (format) in &Determine file type& menu. Once done, press &Load&.
Once the structure is loaded, this is a VMD molecule and you can also load more data into it, creating a trajectory, as explained in the next session.
Loading multiple structures
You can also load multiple structures in a VMD molecule. Let's consider the following example of three Tinker structures:
[user@chembytes]$ vmd -tinker water.xyz water.001 water.002
This command will cause VMD to load water.xyz and load water.001 and water.002 structures into it. The results is a VMD trajectory of three frames. Of course, in case of Tinker, you can create the tinker trajectory with Tinker's archive utility, e.g., water.arc. Since the .arc extension is known by VMD as Tinker format, you can load it directly as:
[user@chembytes]$ vmd water.arc
If you are working with Gromacs, you cannot load directly the .xtc trajectory as for Tinker, but you need to provide also the relative .gro file.
[user@chembytes]$ vmd water.gro water-md.xtc
The trajectory is then loaded into the VMD water.gro molecule. Be aware though that you will have an extra initial frame in your trajectory (water.gro). This can be removed by right-clicking on the VMD molecule and choose &Delete Frames& from the menu.
This can also be done from the graphical interface, specifying in the &Load files for field& in which of the existing molecules the new data must be loaded into. With the graphical interface, if you are loading a trajectory file, you can select which frames you want to load. Data can also be loaded into a VMD molecules right-clicking on it and choosing &Load Data Into Molecule& from the menu.
Save coordinates
VMD allows you to displace/rotate molecules or fragments with respect the original coordinates (see video-tutorial). To save the new coordinates right-click on the VMD molecule and choose &Save Coordinates& from the menu. You will be able to save coordinates in a number of different formats, for all or some frames. Don't be confused between &Save Coordinates& and &Save state&, are two very different things.
Save/Load VMD state
VMD allows to manipulate your structure in a number of way: you can display it (or part of it) in different styles, perform measurements, etc. Once you quit VMD, all what you did will be lost. To avoid this, you can save the state of VMD (File-&Save State) before quit. To reload all your work, start vmd and load the state file you have saved before (File-&Load State)
The default style when you load a structure is: Drawing Method Line and Coloring Method Name. You can change the style from the Graphics-&Representation menu. Also, the same menu will allow you to split your structure in different atoms selections, called Replicas, and display them with different styles and/or hide them. Also, periodic images of the systems can be visualized from this menu. This is one of the widest aspect of VMD and it is quite difficult to cover it by writing. You can read more from the manual, therefore I suggest you to have a look to this video tutorial.
Measure your structure
VMD allows to measure distances, angles and dihedral angle for the selected atoms. To calculate a distance, for example, hit &2& on you keyboard and with the mouse select two atoms. To quit from the distance measurement mode, hit &1&. Hitting &3& and &4& will allows you to measure angles and dihedral angles. Informations about the measurements, as well as their displaying option, can be get from the Graphics-&Labels menu, as mentioned in the VMD slides. Also, for the selected distance, angle or dihedral angle, it is possible to visualize and save in a text file their time evolution, if the measurements are made on a loaded trajectory. Please note that this is a crude way to get geometrical parameters, in particular if you have periodic systems, since the algorithm does not take into account the size of the simulation box.
Move molecules around: the replica mode
VMD allows to displace and rotate molecules interactively dragging them around with the mouse. I just discovered the coolest feature regarding the movement of molecules: the option 9, which allows you to move and rotate a replica. A replica is a view of your system: all the atoms and molecules used in the selected replica, can be moved and rotated. Oh Yeah!!
Transparent background when rendering with Povray
Povray is another wonderful freeware software for astonishing graphical results (if you know how to use it, not like me that use standard VMD settings). VMD allows you to render the scene (vmd's view) you have created with povray (if installed). By default the result is quite good, but if you want to have a transparent background just add the options +ua to the string of vmd parameters used for the rendering.
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xtd转换为xyz坐标，可使用vmd打开
ms的轨迹文件xtd转成vmd等可读的xyz文件脚本
/sobereva/blog/item/852bbefc988504ddfc037fc1.html#0将Material Studio的xtd轨迹文件导出为xyz轨迹文件的方法
文/Sobereva&&First release: 2012-May-23
Material Studio(MS)的xtd文件包含了原子或者粗理化模拟中的bead的轨迹信息。这是MS的私有格式，为了能将轨迹放到其它程序，比如VMD中做更灵活细致的分析，需要转换为通用轨迹格式。xtd文件内含的实际轨迹信息实际上储存在同目录下的同名的.trj隐藏文件里（二进制文件），一种转换成通用格式的方法是利用MS自带的trj2ai.exe程序将.trj文件内容转换成普通文本文件，然后再写个程序将其转换成其它轨迹格式。但这样步骤稍微麻烦些。
另一种做法是直接利用MS内部支持的Perl脚本，循环每一帧每一个原子或Bead，将其坐标属性写入到外部文本文件。比如按照常见的xyz坐标格式来写，就可以生成xyz轨迹了，可以被VMD等程序直接载入。
在/materials-studio上有人提供了现成的这样的Perl脚本将原子轨迹转换成xyz轨迹。我进一步对其进行了修改使之用起来更方便些，另外加入了对周期性体系的支持。脚本如下所示
#**********************************************************
#*& && && && && && && && && && && && && && && && && && &&&*
#*& &&&XTD2XYZ - Convert XTD files into XYZ ormat& && &&&*
#*& && && && && && && && && && && && && && && && && && &&&*
#**********************************************************
# Version: 0.1
# Author: Andrea Minoia
# Date: 08/09/2010
# Convert MS trajectory xtd file into xYZ trajectory file.
# Backup of files that are about to be overwritten is managed
# by MS. The most recent file is that with higher index number (N)
# The script has to be in the same directory of the
# structure to modify and the user has to update the
# variable $doc (line 31) according to the name of the
# file containing the trajectory.
# The xmol trajectory is stored in trj.txt file and it is not
# possible to rename the file within MS, nor it is possible to
# automatically export it as xyz or car file. You should manage
# the new trajectory manually for further use (e.g. VMD)
# Modificator: Sobereva ()
# Date: 2012-May-23
# The range of the frames to be outputted can be altered by line 49 and 51
use MaterialsScript qw(:all);
#open the multiframe trajectory structure file or die
my $doc = $Documents{"./benzene.xtd"};
if (!$doc) {die "no document";}
my $trajectory = $doc->T
if ($trajectory->NumFrames>1) {
& & print "Found ".$trajectory->NumFrames." frames in the trajectory\n";
& & # Open new xmol trajectory file
& & my $xmolFile=Documents->New("trj.txt");
& & #get atoms in the structure
#& & my $atoms = $doc->A
& & my $atoms = $doc->DisplayRange->A
& & # loops over the frames
& & my $framebegin=1;
& & my $frameend=$trajectory->NumF
#& & my $frameend=10;
& & for (my $frame=$ $frame<=$ ++$frame){
& && &&&$trajectory->CurrentFrame = $
& && &&&#write header xyz
& && &&&$xmolFile->Append(sprintf "%i \n", $Natoms);
& && &&&$xmolFile->Append(sprintf "%s %i \n", "Frame",$frame);
& && &&&foreach my $atom (@$atoms) {
& && && && &# write atom symbol and x-y-z- coordinates
& && && && &$xmolFile->Append(sprintf "%s %f&&%f&&%f \n",$atom->ElementSymbol, $atom->X, $atom->Y, $atom->Z);
& && &&&}& &
& & #close trajectory file
& & $xmolFile->C
& & print "The " . $doc->Name . " is not a multiframe trajectory file \n";
使用时先将这些内容复制到一个文本文件里，后缀名改为.pl。然后在MS里将这个.pl加入到项目中。要转换哪个目录下的xtd文件就把这pl文件挪到哪个目录中，并且把my $doc = $Documents{"./benzene.xtd"}; 当中的文件名改成要转换的文件名。之后，保持此脚本文件窗口处于激活状态，选tools-scripting-debug（或者直接按F5，或者按工具栏的蓝色三角按钮）就开始对xtd文件进行转换，转换结束后在当前目录下会输出trj.txt文件。将其后缀改为.xyz之后就能被VMD等程序直接读取了。
debug模式对于大体系、帧数较多的轨迹转换起来颇慢，可以用tools-scripting-Run on server模式来运行，这样转换速度明显快得多，trj.txt将会生成到新的目录，当前目录下的其它文件也会被强行复制过去一份。
此脚本默认转换所有帧。如果想转换指定帧数范围，就把my $framebegin=1;和my $frameend=10;改成自定的起止帧号就行了，需要先将my $frameend=10;前面的注释去掉。
如果是周期性体系，那么在MS当中看起来轨迹是什么样转换过去就是什么样。比如，如果在display style-lattice中在某个方向上多显示一个周期，那么转换出的轨迹在相应方向上也会多出一倍原子。Default、In-Cell、Original的显示模式下转换出的原子坐标也会相应地可能有所不同。
上面的这个名为xtd2xyz脚本只能转换全原子模拟的轨迹，如Forcite的xtd轨迹，却不能转换粗理化模拟的轨迹，如Mesocite的以bead描述粒子的xtd轨迹。我将之修改成下面的xtdbead2xyz脚本，专门用来转换粗理化模拟的轨迹（但不能转换全原子的），用法同前。
# XTDbead2XYZ - Convert the XTD files containing beads into XYZ format
# Creator: Sobereva ()
# Date:& & 2012-May-23
use MaterialsScript qw(:all);
#open the multiframe trajectory structure file or die
my $doc = $Documents{"./bilayer.xtd"};
if (!$doc) {die "no document";}
my $trajectory = $doc->T
if ($trajectory->NumFrames>1) {
& & print "Found ".$trajectory->NumFrames." frames in the trajectory\n";
& & # Open new xmol trajectory file
& & my $xmolFile=Documents->New("trj.txt");
& & #get atoms in the structure
& & my $Beads = $doc->DisplayRange->B
& & # loops over the frames
& & my $framebegin=1;
& & my $frameend=$trajectory->NumF
#& & my $frameend=10;
& & for (my $frame=$ $frame<=$ ++$frame){
& && &&&$trajectory->CurrentFrame = $
& && &&&#write header xyz
& && &&&$xmolFile->Append(sprintf "%i \n", $NBeads);
& && &&&$xmolFile->Append(sprintf "%s %i \n", "Frame",$frame);
& && &&&foreach my $Bead (@$Beads) {
& && && && &# write atom symbol and x-y-z- coordinates
& && && && &$xmolFile->Append(sprintf "%s %f&&%f&&%f \n",$Bead->Name, $Bead->X, $Bead->Y, $Bead->Z);
& && &&&}& &
& & #close trajectory file
& & $xmolFile->C
& & print "The " . $doc->Name . " is not a multiframe trajectory file \n";
这两个脚本文件也可以从此处下载：/c0830hbbpr
转换说明出处
http://www.mdbbs.org/viewthread.php?tid=35210 MS支持客户/服务器结构，用户即使在本地机器建模并提交计算任务，MS也会遵循这个架构，只是把任务提交给本地服务网关而已。
这个结构没有什么稀奇，但是如果经常提交非本地任务的话，经常会出现异常。比如，客户端中止连接或者网络故障，再次打开客户端，有时会无法成功链接远端服务器，造成不能自动回传计算结果。MS帮助说明用户可以自己手工下载结果文件，没有下载也没有存档的计算结果都位于服务器网关目录下，即your MS installation folder\Gateway\root_default\dsd\jobs\下面，文件夹的名称就是任务描述（通常为系统自动分配）。你可以把整个文件夹复制到你本地机器上，可以用MS打开。
根据计算的模块不同，你可能会看到his或者arc文件，他们都是轨迹记录文件，包含位置，速度以及其他体系性质随时间演化的历史。但是你会发现，MS有的模块不能直接处理这些文件。比如，Forcite模块可以分析很多轨迹文件性质，例如，你想得到体系压强随时间的变化，Forcite可以分析。不幸的是Forcite只支持MS本地轨迹文件格式xtd。 帮助文档说明，Forcite还可以分析his和arc格式，但是即使你激活了当前窗口为his动画窗口，Forcite的分析功能仍然是禁用的。
网上搜索相关信息未果。其实解决办法很简单：
1. 在MS中打开或导入his或arc文件；
2. 点击另存为，把his或arc文件存为MS的xtd格式。如果你把xtd存到和his相同的目录，系统会提示你不能复制关联的his文件。你只要换个目录存储就好了。
3. 把存好的xtd(也许包括his)文件移动到原来his或arc文件所在的目录，以后在MS中打开这个xtd，系统会自动调用相关的his或arc。
4. 在xtd为激活窗口的条件下，打开Forcite分析对话框，你会发现所有的分析功能都激活了。
基本的原理是，MS本地xtd格式实际上是一个XML文档，里面仅规定了分子结构和属性列表，真正的历史信息都在与之同名的his或者arc文件里面。真想不通为什么Accelrys不让所有模块直接支持多种轨迹文件格式，非要xtd做个中介！当只有his时，也可将his-xtd-xyz，看上帖就可以
我的也是，楼主知道原因吗？
关于xtd转换为xyz坐标，可使用vmd打开的相关话题在小木虫APP已经有39位虫友给出了详细回复。
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VMD怎么读取data文件？
为了验证自己写的data文件对不对，我想用VMD导入data文件看看，但是不晓得怎么读取？求指点
google sites访问不了啊~
链接打不开，想问直接在VMD里面输入这个命令并不好用提示打不开，输入这个命令之前是否先导入你什么的？或者要操作一些什么呢？
data文件也行嘛？文件类型选什么？自动选择“automatically”时也导入不了耶
你的data数据是从哪个软件里得到的，就对应到下选栏里面选择该软件相关的就行，我用LAMMPS，所以只知道选LAMMPS相关的那个。。。
我也是用lammps里面的msi2lmp导出来的，类型选择lammps trctory也不对呢？文件名*.data不用改吧？麻烦问一下还有什么注意事项吗？我不知道是不是自己哪里做的不对？
额，我是用dump导出来的，导出来的好像是dump.***，这个文件用lammps trajectory没有问题。。。
好吧，没想到google site也被墙掉了。
你可以在网上搜lammps topotools看是否有相关资料。
读取data文件的大致方法是
Extentions -& Tk consoles
在Tk consoles的窗口里cd到你data文件所在的路径，然后
topo readlammpsdata nameofyourfile.data
就可以读取文件了。
若是lammps read_data的文件格式，可以用 topo readlammpsdata data.mean full打开。
注意，这里的full可以改成atomic，molecular, angle等，取决于你的atom_style。
关于VMD怎么读取data文件？的相关话题在小木虫APP已经有380位虫友给出了详细回复。
赶快查看回复吧！
学术必备与600万学术达人在线互动！
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北京学而思教育科技有限公司 地址：北京市海淀区北三环甲18号中鼎大厦A座1层102室 电话：010-
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A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Engineering Molecule Dynamics Simulations on Rapid Solidification and crystal growth of Ti and Ti-Al alloy Candidate : Fu Wei Major : Solid Mechanics Supervisor : Prof. Yang Xinhua Huazhong University of Science and Technology Wuhan 430074, P.R.China January, 2012 独创性声明 本人声明所呈交的学位论文是我个人在导师指导下进行的研究工作及取得的研
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月 华 中 科 技 大 学 硕 士 学 位 论 文 摘 要 Ti-Al 合金作为一类重要合金，具有一系列独特的物理化学特性，被应用到先进
设计之中。而非晶态合金具有比晶态合金更好的强度、韧性、耐磨和抗腐蚀能力，
合金进行热处理得到非晶态合金，可以大大改善其性能，因此有必要研究
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表或撰写过的研究成果，也不包含为获得山东理工大学或其它教育机构的学位或证书
而使用过的材料。与我一同工作的同志对本研究所做的任何贡献均已在论文中作了明
确的说明并表示了谢意。 研究生签名：二马嫉 时间：≥矿，三年多月五阳 关于论文使用授权的说明 本人完全了解山东理工大学有关保留、使用学位论文的规定，即：学校有权保留
送交论文的复印件和磁盘，允许论文被查阅和借阅；学校可以用不同方式在不同媒体
上发表、传播学位论文的全部或部分内容，可以采用影印、缩印或扫描等复制手段保
存、汇编学位论文。 保密的学位论文在解密后应遵守此协议 研究生签名：乌凝 时间：≥口努钿乃自 导师签名： 帆2刀t净占膨日
山东理工大学硕士学位论文 摘要 摘要 本文提出了基于分子动力学模拟研究压力对材料晶体缺陷影响的思路，根据该思
VMD等软件，设计模拟盒子模拟压力对纯金属 A1、Cu 中空位及其它类型缺陷的
具体影响并对结果进行分析。 本文研究了温度对空位类型缺陷的影响。空位发生聚集需要一定的空位密度。在
一定的空位密度前提下，仅施加温度变化的条件时，随机分布的空位会发生聚集生成
不完整的空位四面体缺陷，将变温速度放缓，可以从外形上观察到空位四面体缺陷向
正四面体缺陷转化，结合体系能量分析推测缺陷最终转化为正四面体形状。这种转化
会在面心立方金属中出现而不会在体心立方金属中出现。最高温度弛豫步数太大不利
于形成空位正
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