Intramolecular Moves

To perform Monte Carlo simulations of molecules, you must have a way of changing the internal coordinates of the molecule, e.g. Monte Carlo moves that change bond lengths, angles and dihedrals in a molecule must be performed.

Change into the directory protoms_tutorial/ethane_methanol/gas_phase. In this directory you will see a ProtoMS input file called input.cmd. This input file describes a gas-phase simulation of ethane. Run the input file by typing

$ /path/protoms2 input.cmd

where /path/ is the full directory path to the location in which the protoms2 executable is installed.

This script will have run 500 intramolecular Monte Carlo moves of methane. Look at the trajectory by copying across the snapshot-*.pdb files and viewing them in a viewer like VMD (note that there is a movie.vmd VMD movie file already in this directory in case you are using VMD on windows).

Look at how the molecule moves. The movement is controlled by a z-matrix. This z-matrix is present in the protoms_tutorial/ethane_methanol/in directory. For ethane, it is called ethane.ff. Take a look at this file. There are many different parameters in this file. The z-matrix is contained in the lines;


mode template
solute ethane
info translate 0.0 rotate 0.0
atom  C01 ETH 3000 3000  DM3 DUM DM2 DUM DM1 DUM
atom  C05 ETH 3001 3001  C01 ETH DM3 DUM DM2 DUM
atom  H06 ETH 3002 3002  C05 ETH C01 ETH DM3 DUM
atom  H07 ETH 3003 3003  C05 ETH C01 ETH H06 ETH
atom  H08 ETH 3004 3004  C05 ETH C01 ETH H06 ETH
atom  H02 ETH 3005 3005  C01 ETH C05 ETH H06 ETH
atom  H03 ETH 3006 3006  C01 ETH C05 ETH H02 ETH
atom  H04 ETH 3007 3007  C01 ETH C05 ETH H02 ETH
bond  H02 ETH  C01 ETH flex 0.01
bond  H03 ETH  C01 ETH flex 0.01
bond  H04 ETH  C01 ETH flex 0.01 
bond  C05 ETH  C01 ETH flex 0.01
bond  H06 ETH  C05 ETH flex 0.01
bond  H07 ETH  C05 ETH flex 0.01
bond  H08 ETH  C05 ETH flex 0.01
angle H06 ETH C05 ETH C01 ETH flex 0.5
angle H07 ETH C05 ETH C01 ETH flex 0.5
angle H08 ETH C05 ETH C01 ETH flex 0.5
angle H02 ETH C01 ETH C05 ETH flex 0.5
angle H03 ETH C01 ETH C05 ETH flex 0.5
angle H04 ETH C01 ETH C05 ETH flex 0.5
dihedral H02 ETH C01 ETH C05 ETH H06 ETH flex 15.0

The first set of lines describe how the molecule is constructed, e.g.;

atom  H07 ETH 3003 3003  C05 ETH C01 ETH H06 ETH

this line says that the atom called H07 is bonded to the atom called C05, forms an angle with C05 and C01 and a dihedral with C05, C01 and H06.

Further down in the file is a line that reads;

angle H07 ETH C05 ETH C01 ETH flex 0.5

This says that the angle H07-C05-C01, which is contained in the z-matrix, is flexible, and that Monte Carlo moves that change this angle should be performed, using a maximum angle delta of 0.5 degrees.

Similarly, the line;

dihedral H02 ETH C01 ETH C05 ETH H06 ETH flex 15.0

says that the dihedral H02-C01-C05-H06, which is contained in the z-matrix, is flexible, and Monte Carlo moves that change this dihedral should be performed using a maximum dihedral angle change of 15 degrees.

Question
The protoms_tutorial/ethane_methanol/in directory also contains coordinate and parameter files for methanol. Update input.cmd so that you can run a gas-phase simulation of methanol.

Question
The flex lines in the z-matrix specify the maximum bond, angle and dihedral deltas for intramolecular Monte Carlo moves. The number of accepted and attempted Monte Carlo moves is printed in the output of ProtoMS on lines that look like this;

INFO     Data collection complete. Attempted/accepted moves          100          77

Try changing the bond, angle and dihedral maximum deltas and see if you can improve the quality of sampling of ethane and methanol in the gas-phase.

Do you think that the optimum bond, angle and dihedral deltas would be suitable for use for a water phase simulation?

Content

Intramolecular Moves