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lm-mdanalysis

Some simple fortran codes to analyze molecular dynamics trajectories in DCD formatmdanalysis.tar.gzThis file contains the following analysis programs: align, angles, distance, energy, gss, hbonds, jarzynski, solvation Comments at the top of the corresponding code of each program explain what ... [More] they do. Input files are mostly self-explanatory and are available at the "input" directory. To use these programs, first extract them: tar -xzvf mdanalysis.tar.gz This will create a directory called "mdanalysis", which contains input file examples in the "input" directory. Enter the "mdanalysis" directory and type make to compile the packages, if you have gfortran available. If not, edit the Makefile to define the appropriate compiler. If you have VMD installed, you can also use VMD-style selections by using the shell scripts (ex. energy.sh) scripts. These scripts read the input files which define the groups using VMD-style selections, writes the PDB with the groups definitions as a temporary file and run the appropriate program. Of course this is not a great documentation. Please write to leandromartinez98@gmail.com if you want more information. Globalstructure.fThis code must be compiled with the -m32 option if in 64bit systems in order that the binary DCD files are read. Given a trajectory in DCD format and the corresponding PDB reference structure, computes the following structural factors: 1) RMSD 2) Fraction of native contacts of the atoms, defined as the number of atoms which are closer than some distance in each frame, relative to the number of contacts in the reference frame this contact distance is defined by the 'contact' keyword 3) Gyration radius See the code comments for further information. fitexp.f90This is a package to fit sums of exponentials to time-correlation function data. It uses ALGENCAN as the optimization routine, so please cite it if using this module. ALGENCAN references can be found at: http://www.ime.usp.br/~egbirgin/tango [Less]