md-scripts

Scripts for MD simulation

top2psf.py

A Python code generating a PSF file from a GROMACS top file including gromacs itp files.
The command-line to excute the code will look like:

python3 top2psf.py -f topol.top -o output.psf

bending_modulus

includes C++ codes to estimate bending modulues of lipid bilayers by calculating spectrum of longitudinal molecular orientation fluctuations (https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.028102).
A binary file bend_mod to do spectrum calculation can be compiled as follows:

cd src/

and

make

The command-line to use the generated file will be:

./bend_mod -f input.txt

input.txt has some lines to specify analyzed files and lipids. See a sample file in example directory.
After getting spectrum data with bend_mod, the bending modulus is estimated with the data around small wave numbers. A python code coeff.py can be used to see the spectrum data and to calculate the bending modulus.
The example command-line working in post directory will be:

python3 coeff.py ret_long.dat 310 3

ret_long.dat is the spectrum data obtained using bend_mod. The second and third arguments are temperature and the number of the spectrum data used to compute the bending modulus.

lj3d_education

Training codes (for bachelor students of our group) to run MD simulation of simple lj fluid.
You can simulate the lj fluid consisting of 256 particles in liquid and gas phases by doing

./run.sh

The shell script does compile the cpp files for the simulation and radial distribution function analysis.