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# Random Acceleration Molecular Dynamics (RAMD)                                          *
# Implementation tested on NAMD v2.10 and 2.12                                           *
# December 2017                                                                          *
#                                                                                        *
# Copyright (c) 2017, 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. tcl	        	
                   the latest version of the tcl scripts for running RAMD simulations
2. example/1WDHI        
                   an example for execution RAMD simulations; contains input files and bash script "RAMD-force.sh"
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 


