Setup
=====

Water box
---------

We will use the TIP4P water model; it is considered one of the better
ones as far as reproduction of typical water properties goes. (It is
also the water model to be used together with the OPLS-AA force field.)

Setup Gromacs by sourcing ``GMXRC``.

Generate a small (2.5 nm) water box with genbox_::

  genbox -cs tip4p.gro -box 2.5 2.5 2.5 -o water.pdb 

Note the number of SOL molecules (or count them, e.g. with ``egrep
'^ATOM.*OW' water.pdb | wc -l``).

Edit the topology (``water.top`` file) and enter the number of waters in the
``[ molecules ]`` section.

You can also try using a different water model (such as TIP3P, SPC,
SPC/E) by selecting a different itp file to be included in the
topology file. For these "three point water models" use ``genbox -cs
spc216.gro ...``.


Energy minimization
-------------------

Use the ``em_opls.mdp`` parameter file to set up an energy
minimization ::

   grompp -f em_opls.mdp -c ../top/water.pdb -p ../top/water.top -o em.tpr

and run it::

   mdrun -v -deffnm em

Use the energy minimized system ``em.gro`` as input for the MD simulations.


.. _genbox: http://manual.gromacs.org/online/genbox.html