Go Replicants!

A molecular simulator of Go-type potentials

1 Overview

   Go Replicants! is a molecular simulator for proteins. It uses a replica
   exchange Monte Carlo strategy to explore the energy surfaces of Go-type
   potentials following the methodology explained in Thermodynamics of
   Go-type models for protein folding. Prieto L., de Sancho D., Rey A. The
   Journal of chemical physics. (2005) October; 123:154903.

   This software is currently in alpha stage. Use at your own risk.

   Results at different temperatures

2 Prerequisites

   You need a recent version (1.14 or above) of the GNU Scientific Library.
   It is also recommended to have ATLAS and Gnuplot installed.

3 License

   This software is released under the GNU General Public License. See the
   accompanying LICENSE file for details.

4 Usage

  4.1 Building from source code

    1. Download the package from
       http://curio.mat.ucm.es/~jmbr/go-replicants/go-replicants-latest.tar.gz
    2. Extract the source code with tar xvzf go-replicants-latest.tar.gz
    3. cd go-replicants && mkdir build && cd build
    4. cmake -L ../devel && make

   This builds the binaries molecular-viewer and molecular-simulator.

  4.2 Running a simulation

   You need the structural data of a protein in XYZ format for
   molecular-simulator to operate. Structural data downloaded in PDB format
   from the Protein Data Bank can be converted to XYZ format using a
   conversion script included in the scripts directory. To do the conversion
   write:

 ../pdb2xyz PROTEIN.pdb > PROTEIN.xyz
              

   Once the structural data is in the right format one can run a simulation
   by executing

 ./molecular-simulator -d D -a A -t T1 -t T2 ... -t TN PROTEIN.xyz
              

   In the previous command D and A stand respectively for the dmax and a
   parameters of the potential energy function and T1, ..., TN are the
   temperatures to be simulated (in dimensionless units). This produces two
   kinds of files with extensions .dat and .xyz. The former contain values of
   the potential energy function as the simulation proceeds and the latter
   contain the corresponding spatial conformations of the protein.

5 Bug reports

   Please send bug reports and/or patches to the author's email address.
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