ProtoMS

ProtoMS is a program that can be used to run Monte Carlo simulations. It is very fast and very powerful. It is relatively easy to use, and the manual can be downloaded from here.

If you want to install ProtoMS yourself, you can do so by going to the project webpage and clicking on the downloads tab. You should download the latest current version of the code (currently version 2.22).

ProtoMS can run on Linux, Windows (using cygwin), or Mac OS X. Once you have downloaded the code, untar it using the command;

tar -zxvf ProtoMS_2.22.tgz

(obviously replace 2.22 with whatever version number you downloaded)

To compile ProtoMS, follow the instructions in the README file.

Note that you only need to download and compile ProtoMS is a copy of the program is not already installed on your computer.

Now you should download a set of tutorial input files for ProtoMS. They can be found here. Download and unpack the files and change into the protoms_tutorial/oscillator directory. This contains a simple Monte Carlo simulation of a harmonic oscillator. The simulation is described in the file input.cmd, with the input coordinates coming from the PDB file harm1t2.pdb, and the forcefield parameters in oscillators.ff. The simulation performs one million MC moves on the harmonic oscillator, which should take about 1-3 seconds to complete (ProtoMS is very fast!).

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Question
The average energy of the harmonic oscillator is accumulated from the energies of each configuration of the simulation. The average energy of a harmonic oscillator can be calculated analytically from thermodynamics by using the equation;

E_{average} = 0.5 * k * T

where k is Boltzmann's constant (1.987 * 10-3 kcal mol-1 K-1), and T is temperature (298.15 K). The theoretical average energy should thus be 0.2961 kcal mol-1. How close does ProtoMS get using one million moves?

Question
How many moves does ProtoMS need to run to calculate the correct average energy to 4 decimal places?

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