.. Remember to change the reference "patch" for something unique in your patch file subpage or you will have
cross-referencing problems
In this module we also include a test scenario for GROMACS version 5.1.5 with a possible CG potential and all necessary input files. To run it simply run *gmx grompp -f grompp.mdp -c conf.gro -p topol.top -n index.ndx -maxwarn 5; gmx mdrun* using the patched version of GROMACS version 5.1.5 (see above).
When *gmx mdrun* finished normally (with the above mentioned setup), we have several mandatory checks to see if the simulation was successful or not.
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
Purpose of Module
_________________
One purpose of our project is to promote GC-AdResS as a method. It is an advanced method, for people with experience, and once the simulation is done there are several properties and checks to consider to make sure that the simulation was successful.
This module provides the code to run a velocity velocity autocorrelation function on the current geometries available in the Abrupt AdResS implementation. The paper
`Ref. <http://iopscience.iop.org/article/10.1088/1367-2630/17/8/083042>`_ describes the correlation functions and why they can be used in AdResS. This code is based on that theory and has been developed to check the dynamics of the local thermostat GC-AdResS simulations presented in the paper cited above.
Source Code
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.. Notice the syntax of a URL reference below `Text <URL>`_
Files are stored here: `<https://gitlab.e-cam2020.eu/krekeler/analyze.energy>`_. The source code for the velocity autocorrelation function can be found here: `<https://gitlab.e-cam2020.eu/krekeler/analyze.energy/tree/master/app/cal_vel_acc_adr.cpp>`_
The installation instruction can be found `<https://gitlab.e-cam2020.eu:10443/krekeler/analyze.energy#installation-instructions>`_.
Usage:
::
cal_vel_acc_adr:
options:
-h , "print this message")
-b start time
-e end time (=number of MD steps)
--x0 lower bound of the interval
--x1 upper bound of the interval (--x1 0, use the whole box = atomistic)
--frame length of correlation
--acc breaks
--total number of frames
--tf Output Frequency (=Delta_t)
-m type of simulation to analyze (adress or atom)
-f input .xtc file
-o output file
It is important to have the XDR files and setup in the same directory as they have to be specified in the Makefile. The XDR files can be found via the GROMACS web page, see `<http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library>`_ or `<ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz>`_.
