Nine Rivers

While running a command line program or some GUI initiated from command line on Windows, there is always a black console window on the screen. This sometime becomes annoying. For example, when you start the Eric Python IDE on Windows, normally you start it by calling a batch file “eric4.bat” which calls the actual eric4.py script sequentially. Since Eric4 is designed to be a GUI program, the black console window has no use but it is there. To prevent that or hide it, there are several ways. [Read the rest of this entry...]

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.

Not all websites have links to “printable version” like wikipedia. Although many websites have stunning  look, it is really ugly when you try to print them. Some parts of the pages will be missing or the format is totally a mess. Instead of waiting the website owner realize this and prepare printer friendly pages for you, you can try to use the “web developer” firefox plugin to solve this problem. Just install the plugin,  then on the web page you would like to print, right click your mouse and find the menus shown in the following picture, choose display CSS only for printer. The web page will become fluid and ready to be printed. [Read the rest of this entry...]

I’m using Pidgin v2.7 and Windows XP. I’ve tried most of the methods flying on the internet about changing themes for Pidgin, but none of them works. These include using the gtkthemeselector.exe. I noticed the latest Pidgin using a  “%APPDATA%\.purple\gtkrc-2.0″ to control the look and feel once the “GTK+ theme control” plugin is enabled. The contents of this file look very similar to the contents of the theme files under “c:\program files\common files\gtk\2.0\share\themes\***\gtk-2.0\gtkrc”. I tried to copy the contents of gtkrc file of the “Clearlooks-DarkLime” theme and pasted them to the “%APPDATA%\.purple\gtkrc-2.0″. After restarting Pidgin, I saw this
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For gnuplot version older than 4.4, ‘plot for’ is not an option to plot multiple files. In order to make it work and easier, I wrote a BASH script to generate the gnuplot input for multiple file plotting. You are lucky too find this if you are still using old version of gnuplot. No need to use it for the lastest version.

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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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I occasionally got this error while running some mpi programs. I could not find the exact reason. Even when I google it, it seems no relevant explanation of it. By investigating the codes with debugger, I notices some data in the memory are huge, when I correct them, the error information was gone too. Therefore I guess this error is related to the expression of illegal numbers. However, I would like to know more about it if someone can point out the exact reason.

DeinoMPI is an implementation of MPI-2 for Microsoft Windows. DeinoMPI is a derived work from MPICH2 provided by Argonne National Lab.  By starting with the MPICH2 code base DeinoMPI inherits a stable and complete implementation of the MPI-2 standard.  DeinoMPI heavily modifies the original code base and does not rely on anything from Argonne National Lab.

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According to the article “Mounting smbfs Shares Permanently Help File” published on JustLinux by Ray Cowan, we could mount a Windows shared folder automatically using /etc/fstab. There are many discussions about how to do this on the internet. E.g. some people suggest using ~/.bashrc or ~/.bash_profile to fulfill this. But there are not the right solution. Because the mounting should only be done once not more. The essential thing in Ray’s article is one can use options of smbmount command in fstab. The working format looks like

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