Commit b6df8350 authored by Christian Krekeler's avatar Christian Krekeler

rewording&typos&moving

parent a269541a
......@@ -246,9 +246,10 @@ Another important aspect is the force capping. Abrupt AdResS works fine for smal
The local thermostat simulations are significantly different from the Abrupt coupling AdResS simulations. The atomistic region is indirectly thermalized by the hybrid/coarse grained, which leads to an NVE-like environment. To make sure the simulations run smoothly, a tabulated potential for shifted Lennard-Jones potentials is needed. Furthermore, GROMACS has to be compiled with double resolutions. It is easy to see when the simulation didn't work, as the atomistic region is evacuated by all molecules and the resulting density has an error of around 50% and higher.
When the simulation worked, the same checks as for Abrupt AdResS are required. The first check is about the density: if you have no thermodynamic force you will have rather pronounced spikes in the density at the interfaces. If you have a converged thermodynamic force the density has to be within +/- 3% (optimal) and +/- 5% (still valid) off from a comparable full atomistic simulation / experimental data. However, an "artificial" interface is introduced and checks for the diffusion, the RDFs, etc. (full list see below), ensure that the regions mix toghether and that you have proper particle transfer.
When the simulation worked, the same checks as for Abrupt AdResS are required. The first check is about the density: if you have no thermodynamic force you will have rather pronounced spikes in the density at the interfaces. If you have a converged thermodynamic force the density has to be within +/- 3% (optimal) and +/- 5% (still valid) off from a comparable full atomistic simulation / experimental data. However, an "artificial" interface is introduced and checks for the diffusion, the RDFs, etc. (full list see below), ensure that the regions mix together and that you have proper particle transfer.
This is an example of test scenario for GROMACS version 5.1.5 with a possible CG potential and all necessary input files, see `<https://gitlab.e-cam2020.eu:10443/abrupt_adress/abrupt_adress>`_ . 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).
......@@ -273,7 +274,6 @@ The patch for Abrupt_AdResS can be found here:(:ref:`localT_abrupt_adress`)
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, see `<https://gitlab.e-cam2020.eu:10443/abrupt_adress/abrupt_adress>`_ . 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* finishes normally (with the above mentioned setup), we have several mandatory checks to see if the simulation was successful or not.
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