insilicoengine

GNUPLOT is very easy tool to plot the data in nicer way! How to plot data from file ' data.dat ' for total row lets say 2000? --> Traditional way p " data.dat " u 1:2 w l or plot " data.dat " using 1:2 with line But, How to plot data for row from 1000 to 2000? --> p [1000:2000][] " data.dat " u 1:2 w l So far this is easy. Right? Now how to plot data for row from 1 to 1000 and 1001 to 2000? Hmm... Quit tricky. Lets do the following: [use some bash scripting ;-)] --> p  "<(sed -n '1,1000p' data.dat )" u 1:2 w l, \     "<(sed -n '1001,2000p' data.dat )" u 1:2 w l Old  New

In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f  xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]

Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========

CATDCD program can be used to convert one file format to another file format. For example: How to convert trajectory output of GROMACS .xtc format into NAMD .dcd format ==== /path/to/catdcd -o /path/to/save/file/abc.dcd -xtc /input/path/to/save/file/abc.xtc ==== How to install CATDCD? Follow the link-   https://www.ks.uiuc.edu/Development/MDTools/catdcd/ Download the catdcd-X.Xx.tar.gz Extract all files from the tar. Locate the catdcd file. It should be in directory :  catdcd-4.0b/LINUXAMD64/bin/catdcd4.0/ Source the catdcd in your bashrc: export PATH="/path/to/catdcd/directory/:$PATH"

SAGEMATH It is an open source Mathematics software created by people who use it everyday. It is developed by mathematician doing research in math at universities. It is good because it is totally free, not like Mathematica which is expensive and closed source. Closed source means you don't have an idea of their working and you can not modify them. As Mathematica is very expensive, it is a real issues for the universities and for the developing countries to buy their licenses and install to teach to the students or to use it in research. No doubt SAGEMATH is playing a huge role in this aspect and that's the reason SAGEMATH is rapidly expanding. Download: http://www.sagemath.org/download.html Installation of SAGEMATH: Please follow the following links for the installation. http://doc.sagemath.org/html/en/installation/ Several packages has been installed during SAGEMATH installation. alabaster-0.7.12.tar.gz appnope-0.1.0.tar.gz arb-2.16.0.tar.gz Babel-2.6.0.tar.gz back

NUDOKU ( https://github.com/jubalh/nudoku ) # yum install nudoku [On RedHat based systemes] # dnf install nudoku [On Fedora 23+ versions] $ sudo apt-get install nudoku [On Debian based systems] 2048 ( https://github.com/tiehuis/2048-cli ) On Centos/Fedora # yum install 2048-cli-nocurses # dnf install 2048-cli-nocurses [On Fedora 23+ versions] On Ubuntu sudo apt-get install libncurses5-dev $ sudo apt-get install libsdl2-dev libsdl2-ttf-dev $ sudo apt-get install 2048-cli MyMan/ Pac-man ( https://myman.sourceforge.io/ ) GREED ( http://www.catb.org/~esr/greed/ ) $ sudo apt-get install greed Pacm4console ( https://sites.google.com/site/doctormike/pacman.html ) # yum install pacman4console # dnf install pacman4console $ sudo apt-get install pacman4console MoonBuggy ( https://github.com/seehuhn/moon-buggy ) # yum install moon-buggy # dnf install moon-buggy $ sudo apt-get install moon-buggy Robot Finds Kitten ( http://robotfindskitten.org/ ) NLNVADERS ( htt