March 30, 2012, 2:38 pm
I’m doing molecular modeling and simulation in chemistry and material science. The words “modeling” and “simulation” are often used interchangeably in my texts. However, more precise distinction must be made in scientific publications. Beat Schwendimann gave clear definitions of them. (I quoted his texts below)
The original post is here: http://proto-knowledge.blogspot.com/2010/12/what-is-difference-between-simulation.html
Continue reading ‘Difference between modeling and simulation’ »
February 28, 2012, 6:42 pm
I drew this self-portrait in 20 seconds with the amazing ScribblerToo by zefrank. This small flash gadget implements a simple but very catchy shading effect by introducing extra thin lines based on the line drawing by the users. You can find a lot of wonderful work on the internet if you search its name at Google.
Continue reading ‘Mini-me by amazing tool ScribblerToo’ »
February 25, 2012, 5:21 am
Don’t know where I found this (possibly on Google+). Very encouraging! But I think Nike’s slogan is more concise and conveys essentially the same meaning, “Just do it!”
February 24, 2012, 7:57 pm
This is not even a tip of VMD, because it should have been known by most of the experienced VMD users. However, in case you are new to VMD or still do know these, you will be happy for seeing this post.:)
- Use the GUI menu:
First, click menu “File->New Molecule …” to read the coordinate file. E.g. test.xyz or test.pdb;
Then click menu “File->Load Data into Molecule …” to load the structure file, e.g. test.psf
- Use tcl commands:
This is a more flexible way.
In the command window, type “mol new test.pdb” to load the coordinate file then “mol addfile test.psf” to load the structure file.
This can be simplified with one command “mol load psf test.psf pdb test.pdb“.
Continue reading ‘Ways to load structure and coordinate files into VMD’ »
February 24, 2012, 1:35 pm
In MS Word 97, you could insert data & time by clicking the ‘Date & time’ button on the insert->text panel. This will by default insert a dynamically updated field that shows the ‘current’ date (when this field is updated. Why is it the current date? because this field will be automatically updated when you open the document.) and time. This is straightforward for most of people.
However, in some cases we need a different update strategy. For example, I have a work note in which I add notes to record my daily work progress. I would like to put a date on top of this document to remind me when it is updated. I could not use the date field mentioned above, otherwise the date field will be updated each time I open the document but not each time I modify it. The solution is to use the other field named ‘SaveDate‘ in place of field ‘Date’. You could find it in “insert menu->quick parts->field (check the data and time category)”. With this field each time I save the document the field is updated. That’s what I want for my work note.
December 2, 2011, 7:16 am
create ~/.bash_logout
with the following contents:
1
2
| t=`readlink -f \`pwd\``
ln -sfn $t ~/lastdir |
Each time when you log off, the current dir is remembered and a symlink is created in ~/ .
It’s convenient for the next time:)
NOTE:
1. “readlink -f” to ensure you ALWAYS get the really full path (or you will have recursive symlink if you are leaving a path with smylink in it)
2. “ln -sfn” allows you to overwrite the existing symlink
November 18, 2011, 2:22 pm
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：
1. Kremer版： 特点是用一个WCA势函数作为“硬核”。不方便的地方是，势能的极小值与硬核势的参数有关，不是十分直观。同时这个势函数关于势能极小值是非对称的。
Continue reading ‘FENE势函数的函数图像和不同版本’ »
November 16, 2011, 7:26 pm
The Ubuntu CD contents look like these:
There is an executable named “wubi.exe”, which allows you installing Ubuntu alongside with an existing Windows system (dual-boot). However, many people experienced “no response” problem after double clicking the wubi.exe. Some say this is because some of your drives contains non-English labels. However, this is not always the case. On my Windows I have all drives with English names, but I couldn’t get wubi.exe run.
The solution came from this post of Grizzly. Because there are several versions of Python installed on my Windows, and surely the PATH and PYTHONPATH are set with multiple values. Apparently wubi.exe is interfered by these environment variables. After setting them to empty, I got wubi.exe run! (In fact I only had to set PYTHONPATH to empty) Then you should see the picture below.
Continue reading ‘Ubuntu wubi.exe installation’ »
November 15, 2011, 9:38 am
