Solvent Rigid Body Moves

Molecular simulation nearly always requires modelling of solvent. Solvent plays a key and often little understood role in many molecular and biomolecular processes, and its correct modelling is crucial to allow the results of molecular simulation to be properly compared with experiment.

Solvent in Monte Carlo simulations can be modelled in many ways. The most common is to use an explicit model of the solvent. This means that a model of each solvent molecule is constructed, and these molecules are used to solvate the solute or system being studied.

Change to the protoms_tutorial/ethane_methanol/solvated directory. This contains an input.cmd file that runs a simulation of ethane solvated in a periodic box of water molecules. The TIP4P model is used to represent water. Run the simulation by typing;

$ /path/protoms2 input.cmd

(remember to replace /path/ with the full directory path to your protoms2 executable).

Visualise the resulting snapshot PDB files from the simulation using a molecular viewer such as VMD (and again, a movie.vmd file is already provided for you if you are using VMD on windows).

You will not see much movement in the simulation because it was very short. However, what you should see is that the water molecules move as rigid bodies. ProtoMS moves solvent molecules using rigid body translation and rotation moves. The maximum amount to translate and rotate each solvent molecule is set in the parameter file for the solvent. This is contained in the file protoms_tutorial/ethane_methanol/in/solvents.ff. This contains parameters for many different solvent molecules. The relevant lines for the TIP4P water model are;

#
# TIP4P (T4P)
#
#     O00       dist(OH) = 0.9572 A
#   /  |  \     dist(OM) = 0.15 A
# H01 M03 H02   ang(HOH) = 104.52 deg
#

mode clj
par 2003  OW  8  0.000  3.15363  0.1550
par 2004  HW  1  0.520  0.0      0.0
par 2005  ??  0 -1.040  0.0      0.0

mode template
solvent T4P
info translate 0.15 rotate 15.0
atom O00 2003 2003
atom H01 2004 2004
atom H02 2004 2004
atom M03 2005 2005

These lines provide the change and Lennard Jones parameters for each of the atoms in water. They also provide the maximum amount by which to translate and rotate the molecule, e.g.

info translate 0.15 rotate 15.0

means that each water molecule will be translated by a maximum of 0.15 angstroms, and rotated about a random vector by a maximum of 15 degrees.

Question
Increase the number of Monte Carlo moves performed during the simulation. This is specified in the input.cmd file. Increase the number until the movie shows that the waters are diffusing through the box.

Question
Edit the input.cmd file so that you can simulate methanol in a box of water. Run a long simulation to allow the water to equilibrate around the methanol. How does the water structure around the final snapshot from the simulation of methanol compare to the water structure from the final snapshot from the simulation of ethane?

Question
Edit the z-matrix of ethane and methanol to change the bond, angle and dihedral maximum deltas. Try to optimise these values to get a good acceptance ratio and to get a large amount of motion of the solute. Also edit the solvents.ff file to change the translation and rotation deltas of TIP4P. Again, aim to get the most motion of the water, while keeping a high acceptance ratio (about 50-60%).