Energy (AT)/Energy(interface) ratio: Necessary condition for AdResS simulations¶
Purpose of Module¶
One purpose of our project is to promote GC-AdResS as a method. It is an advanced method, thus 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 check one very important quantity, the interaction energy in the atomistic region compared with the interaction energy in the comparable subregion in a full atomistic simulation. The difference between those energies is the interaction energy at the interface, which has to be much smaller than the interaction energy in the atomistic region.
The theory is described in Ref.. This legacy code is based on that theory and has been developed to check the energy of the local thermostat GC-AdResS simulations presented in the paper cited above.
Running the code:¶
The executable is called energy. The options on how to run the analysis:
-h : help message
-b : start frame
-e : end frame
-n : number of regions
-x0 : start transition region
-x1 : end transition region (if x1 == 0, use the whole box)
-q1 : charge on oxygen
-q2 : charge on hydrogen
-sig : sigma
-eps : eps
-beads : no. of beads in one ring polymer
-c : cut off radius for neighbor list search
-f : the input .xtc file (default: traj.xtc)
-o :the output file
Source Code¶
Files are stored under https://gitlab.e-cam2020.eu/krekeler/analyze.energy. The source code for the energy calculation can be found at https://gitlab.e-cam2020.eu/krekeler/analyze.energy/blob/master/app/energy.cpp. The installation instruction are available at https://gitlab.e-cam2020.eu:10443/krekeler/analyze.energy#installation-instructions.
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.