Some resources and analysis scripts for Molecular Dynamics simulations

• MARTINI_CHOLESTEROL_NAMD.zip: NAMD-formatted topology and parameter files for Coarse-Grained cholesterol, based on the original MARTINI model (Marrink et al, J. Phys. Chem. B 2007, 111 (27), 7812-7824).
• MARTINI_PIs_NAMD.zip: NAMD-formatted files for three PI lipids, intended for use with the MARTINI and PACE force fields. Based on the equivalent GROMACS parameters, as presented in Lopez et al, JCTC, 9:1694–1708, 2013.

• Divalent_Metal_ions_GMX..zip: Parameters for divalent metal ions (Fe2+, Mn2+, Mg2+, Be2+ etc) in GROMACS format for use with the TIP3P (CHARMM, AMBER) and SPC / SPCE (GROMOS) water models. Based on the work by Li et al, J Chem Theory Comput 2013, 9(6):2733–2748.

• GMX Jarzynski (Python 3.x): A Python 3.x script to perform Potential of Mean Force (PMF) calculations using Jarzynski's equality, for pulling simulations generated by GROMACS. Useful for analyzing Steered Molecular Dynamics (SMD) simulation data and doing a "quick and dirty" estimation of a PMF, although it will never be as accurate as good old Umbrella Sampling or Free Energy Perturbations.
• GMX Jarzynski (Python 2.7): The same script but for the (soon to be obsolete) Python 2.7 version.

Note: Scripts should be loaded in PyMOL using the "Run Script" functionality. See the appropriate PyMOLWiki page for more information.

• Cremer-Pople Carbohydrate Ring Puckering calculator (for PyMOL 2.1 or later with Python 3.x) support: A Python 3.x / PyMOL script that implements functions for performing Cremer-Pople (CP) puckering calculations for carbohydrate rings. The method is based on the approach presented by Hill and Reilly in Hill, A.D., Reilly, P.J. (2007) Puckering coordinates of monocyclic rings by triangular decomposition.J. Chem. Inf. Model. 47(3):1031-5, doi: 10.1021/ci600492e. This version of the script is for any PyMOL 2.x versions that are built upon Python 3 (both commercial and open-source versions). Users of PyMOL 1.5 and/or 2.0, built upon Python 2.7, should use the 2.7 version of the script, displayed below.
• Cremer-Pople Carbohydrate Ring Puckering calculator (for PyMOL 1.5-2.0 or later with Python 2.7) support: The same script, built for PyMOL versions that use Python 2.7. The script may work for the legacy De Lano versions (0.98-1.2), but it has not been tested enough for them.

• Karplus Equation Calculator: A Perl script that uses the Karplus equation to predict J-couplings based on dihedral angle calculations from MD simulation data, as produced by the GROMACS "gmx angle" utility. Useful for analyzing dihedral angle measurements of carbohydrate simulations.