Molsim

MOLSIM is an integrated MC/molecular dynamics/Brownian dynamics simulation package created by Per Linse in Lund. Version 6.4.7. of Molsim is beeing further developed and extended using this git.

Obtaining the Code

There are two possibilities of how to obtain the code. You can either simply download the zip of the code, or clone the whole repository.

Downloading the Zip

Download the zip from here and save it in the directory of your choice. Afterwards, navigate to that directory and extract the source code with

unzip <name of the zip file>

You might want to rename the directory to some more reasonable name.

Clone the Molsim repository

Just run

git clone https://github.com/joakimstenhammar/molsim.git

If you set up your ssh key at GitHub you can run

git clone git@github.com:joakimstenhammar/molsim.git

Installation of Molsim

Navigate into the Molsim directroy and run the configure script. This will check some dependencies. Molsim requires FFTW 3.3.4. In can be install automatically within the configure script (Note: This might take some time). The configure script will also ask you for a version name. This version name will be appended to the executables of molsim (molsim_ser.ver instead of molsim_ser). Leave it blank for no special version name.

cd Molsim
./configure.sh

The configure script tries to locate the FFTW libary. If you want to customize the path of the libary, modify the Src/make.fftwpath file. Additionally it will select which compiler to use. To costumize the compiler which is to be used change the Src/make.arch file.

Now make Molsim:

make all

For more details confer the MOLSIM manual.

Usage

Confer the MOLSIM manual for the standard commands.

Additional Notes

• Cygwin
  • To install FFTW in cygwin you can either install it with the configure script (slow), or install the package libfftw3-devel. Either way you have to run updatedb afterwards to update the database of your file system.