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# 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 


