*************************************************************************** # Random Acceleration Molecular Dynamics (RAMD) * # Implementation tested on NAMD v2.10 and 2.12 * # July 2018 * # * # Copyright (c) 2018, HITS gGmbH * # (Heidelberg Institute for Theoretical Studies), Germany * # Authors: Vlad Cojocaru, Stefan Richter, Daria Kokh, Rebecca Wade * # Email: mcmsoft@h-its.org * #************************************************************************** ---------------Random Acceleration Molecular Dynamics--------------------- RAMD 5.0 implementation tested in NAMD 2.6, 2.7b2, 2.10 and 2.12 Note that to be able to estimate dissociation rate constants (koff rates) using the tauRAMD method as described in the following publication : Kokh et al., J. Chem. Theory Comput. (2018), DOI: 10.1021/acs.jctc.8b00230 https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00230 one needs to download additional scripts for processing the RAMD trajectories from the HITS website: https://www.h-its.org/downloads/ramd/ Distribution contains: 1. scripts the latest version of the tcl scripts for running RAMD simulations 2. examples/1WDHI example for execution of RAMD simulations; contains input files and bash script "RAMD-force.sh" examples/DCL example for execution of RAMD simulation; converted from RAMD-4.1 release 3. TRJ-Analysis-R (if downloaded from https://www.h-its.org/downloads/ramd/) R script for computing relative residence times from RAMD simulations (tauTAMD method); application example for HSP90