can you please guide me how to install Gromacs and how to work with it.? I want to use Gromacs for the protein simulation.
To install Gromacs you need to choose weather you are going to use windows version or linux version, however, I used on linux and it easy to install, you need to follow the instructions in the installation guide. Further, to work with this software you should do first tutorials available on the website of Gromacs, these are very easy.
Thanks Abhishek,
I want to work on windows, i downloaded it from the web, it gave gz file. So can you please provide more information, that how can i install it.
okay,
1. Gromacs Installation: Video guide to install Gromacs on Linux
https://www.youtube.com/watch?v=bxWjWmdf6xw
https://www.youtube.com/watch?v=vOJsmtFeSGk (1-5 steps)
2. How to install GROMACS on windows
1. Download cygwin from http://www.cygwin.com/
a. click on the link to "install from internet" and run the installer
b. when you get the dialog that asks you what packages to install expand and select "gdn" "gdb" and "make"
c. follow the rest of the installation instructions
EDIT: this website has a pictorial guide to install the packages with cygwin. I forgot to mention they are all under Developer, so expand that first.
EDIT: also install the tcsh package
http://www.eecg.utoronto.ca/~aamodt/ece242/cygwin.html
2. Next you are going to need the GROMACS source code. You can get it here.
a. download and save the file someplace handy
3. Next you need FFTW. There are pre-compiled dlls for Windows, but I would recommend not using them unless you know how to set the path variables. The easiest way is to grab fftw-3.2.1.tar.gz . Again, save this someplace handy.
4. create a folder someplace (C:\FFTW) and extract FFTW to it.
5. start cygwin and change the directory to your FFTW folder: cd c:\fftw
6. type: ./configure --enable-threads --enable-sse --enable-float
7. then: make
8. then: make install
9. now create a folder for gromacs (C:\gromacs) and extract the distribution there. There should be a few folders like admin, src, etc.
10. in the cygwin console, change your directory to the gromacs folder: cd c:\gromacs
11. type: ./configure --enable-shared LDFLAGS='-L/usr/local/lib'
12. then: make (this took a couple of hours to run through)
13. then: make install
14. make links
15. make clean
when you get your prompt back in cygwin (or from a fresh session change your directory to c:\gromacs) type: luck
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