FENE势函数的函数图像和不同版本
FENE（finitely extensible nonlinear elastic）势函数可以用来描述分子成键相互作用。它的主要特点是最大键长只能有限值，这是和harmonic成键函数的主要不同之处。文献中有两个常用的版本：
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Archive for the ‘分子模拟’ Category.
density profile的计算
1. Gromacs有一个工具g_density可以分析各个方向上原子的数密度和电子密度。
2. VMD有一个第三方插件VMD Density Profile Tool,可以根据原子类型分析密度分布。
3. LAMMPS的Pizza工具包有一个脚本density.py也可完成类似工作。
可根据需要选取。
Compile gromacs on Cygwin
Just some notes:
1. manually download and install fftw3. Do not use the cgywin package, or the path will not be recognized by Gromacs.
2. Needed Cygwin packages: lapack, gcc, g77, make and nasm. nasm is required for both fftw and Gromacs in order to compile the assembly codes.
Nonbond interactions in Materials Studio and unit conversion
1. by default, while using cff91, 1-2, 1-3 pairs are excluded. But 1-4 pair is considered as nonbond pairs. This is valid for both vdW and electrostatic interactions.
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Display dihedral angle in PyMOL
An alternative and better ways is to use the ‘distance’, ‘angle’ and ‘dihedral’ commands of ‘cmd’ object. Note not using ‘get_distance’, ‘get_angle’ and ‘get_dihedral’, they are for different purpose. The syntax is e.g. ‘dihedral dih_obj_name, id 1, id 2, id 3, id4’, i.e. giving an object name and four atom selections. (In this example, we use atom IDs for atom selections. Other syntax for atom selection should work too.) Using this method, the measurement will be automatically updated while playing the movie
Twitter的生活
很早就有Twitter和Facebook的帐号了，但是一直没有热情使用他们。因为自己是在不是那种需要告诉朋友自己早餐吃了什么的人。不过这两个如日中天的SNS服务，在某些专业领域也有独特的用途。例如，在facebook上就可以找到关于分子模拟的组群，便于大家快速分享消息。因此，最近打算尝试一下。我在Twitter上的帐号名称为“SimuWorld” (Facebook也相同), 有兴趣交流的朋友可以找我。
Notes on compiling lammps on linux
To compile Lammps, we needs fftw 2.x library. The latest is fftw 3.x which is not compatible. Go here and download fftw2.
If you don’t have root privilege on the server, meaning you cannot install the library to the default system path (/usr/lib,/usr/include), you have to specify a prefix before making the library. Simply do this in the source directory, “./configure –prefix=/your_parth/fftw2″. Then “make” and “make check”, “make install”. These commands compile and install fftw library under the path you give.
Compile DL_POLY
The first time I compile a true Fortran program;) On my Debian pc, I installed gfortran and downloaded a copy of the famous DL_POLY. Maybe I was blind, I did find an instruction on how I should compile it. Compared to the previous version, version 2.19 has a different directory organization. Istead of ‘source’ I found the ‘srcmod’ should be the place hiding the treasure. You have to copy the make files from the build folder to this folder. Then, a problem which made me waste some time on was I have to rename the MakeSEQ or MakePAR to ‘makefile’. Believe or not I tried different name but with ‘make -f othername’, I failed with an error “no target seq”. Normally it should be not a problem if I specify a makefile name explicitly other than ‘makefile’. I don’t understand this. After this, I had no any trouble with the compilation.
A new portal website for computer simulation
很早就计划做一个专门关于分子模拟的论坛。目的是转播、交流关于分子模拟技术的进展，应用，并给 这个领域工作的朋友们提供一个探讨科学问题的园地。我相信共同讨论是一种最佳的学习途径，同时也是发现错误最直接的方式。这也许就是中国谚语中“听君一席 话，胜读十年书。”在现代互联网世界的一种诠释吧。
最近很多论坛软件都做了更新，象以前用过的SMF，Drupal都有重要升级版。考虑到以后论坛的发展，Drupal再次成为最终选择。因为它不仅增强了论坛功能，同时它作为一个综合的门户CMS软件，也有许多不可取代的优势。
安装过程简述如下：
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