GROMACS suit of programs use van der Waals (vdW) radii of atoms and or molecule for different operations. However, no reference is supplied for the values used in the $GMXLIB/vdwradii.dat (you can use ‘locate vdwradii.dat’ in terminal to get absolute (more…)
The 4.6.x branch of GROMACS has switched to CMAKE build system. The CMAKE system has streamlined the compilation process, and has the added benefit of the optional very user friendly interface that is a part of CMAKE, ccmake or gui-cmake.
Here the (more…)
There are many programs to visualize PDB and or other molecular structure files. Among these, PyMOL and VMD are some of the best. Both are free for academic work and available on a wide range of platforms. Both programs can be downloaded from their respective (more…)
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular simulation suite that can be used to simulate proteins, lipids and nucleic acids. GROMACS is one of the fastest and most popular packages available, it is open source, free, and available (more…)