samech-git / lammpstutorials

LAMMPS tutorials for simulations with the ELBA model

LAMMPS Tutorials

This repositoty contains LAMMPS tutorials for simulations with the ELBA model.

For now it contains the following tutorials

1. Membrane - simulation of a DOPC membrane with the ELBA potential
2. ElbaSolv - solvation free energy calculation of an ELBA water in a box of ELBA water molecules

It is assumed that you have downloaded the Scripts repository from my Github account. This can be accomplished with

git clone https://github.com/SGenheden/Scripts

In the tutorials, I will refer to the location of the Scripts folder with $SCRIPTS.

Installing LAMMPS

We will start with installing LAMMPS. We will use my own version of LAMMPS hosted on Github. It contains some of my modifications to the code and it will be required by some ELBA tutorials. Some of the modifications will eventually be released in the official version of Lammps.

Clone my lammps repository from Git hub

git clone https://github.com/SGenheden/lammps

Next, we will install the colvars library that is needed for some simulations

cd lammps/lib/colvars
make -f Makefile.g++

Now we are ready to install LAMMPS. By default LAMMPS will only contain a limited set of functional. The rest of the functionality can be accessed by installing a set of packages. You can read more about packages here. Therefore, we will start to add the necessary packages for ELBA simulations

cd ../../src
make yes-dipole yes-kspace yes-manybody yes-misc yes-molecule yes-rigid yes-user-colvars
cp USER-MISC/angle_dipole.* USER-MISC/pair_lj_charmm_coul_long_14.* USER-MISC/pair_lj_sf_dipole_sf.* .

The last command add a few bits from the USER-MISC package. This is a large package with user-contributed code and it is unnecessary to install all of it.

To compile LAMMPS we need an appropriate make file. One that work with the OpenMPI and Intell compilers on Southampton machines/clusters can be found in this repository. Copy the file Makefile.soton to the lammps/src/MAKE folder and then execute

make -j 8 soton

The installation should end with something like this

size ../lmp_soton
   text        data     bss     dec     hex filename
8478121      176400   18176 8672697  8455b9 ../lmp_soton