Commit 043e94aa authored by Christian Krekeler's avatar Christian Krekeler

data from old library

parent a62fb395
.. _abrupt_adress_patch:
####################################
Patch file for module: Abrupt AdResS
####################################
......
......@@ -45,7 +45,7 @@
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _example:
.. _abrupt_adress:
#######################################################
Abrupt GC-AdResS: A new and more general implementation
......@@ -139,7 +139,9 @@ Here is a short manual on how to run the test and set up AdResS simulations in G
2) You need a very well converged NVT run, which can be used as starting point for the coarse grained (CG) and then later the AdResS simulations.
3) You have to generate a coarse grained (CG) potential. We use, for convenience, the inverse Boltzmann iteration provided in the VOTCA package (`<http://www.votca.org/home>`_). The resulting tabulated CG potentials are used in the AdResS simulation. Alternatively you can use WCA potentials or standard Lennard-Jones potentials. The main requirement for the AdResS simulation is that the density in the CG region is the same as in the atomistic (AT) region.
NOTE: The method can be used with any potential, which preserves the correct density. If only a SPC/E CG potential is available it can be used for SPC/e water models as well as for a more advanced water model. It is possible to use a WCA potential, which is basically a Lennard-Jones potential. *And* it is possible to switch the CG ptential completely off. That will transform the CG region to a true thermodynamic reservoir with a non-interacting gas.
4) The next step is to create a double resolution configuration and adjust the dependncies (force field, topology, index file, GROMACS input file). Creating the configuration is straight forward (we use `<http://www.votca.org/home>`_).
::
......@@ -214,7 +216,7 @@ Furthermore, in our simulations we use:
vdw-type = user
rvdw = 1.0
In case of local thermostat simulations (see `(for J.Chem.Phys.): <https://aip.scitation.org/doi/10.1063/1.5031206>`_ or `(for arXiv): <https://arxiv.org/abs/1806.09870>`_) we use:
In case of local thermostat simulations (see `<https://aip.scitation.org/doi/10.1063/1.5031206>`_ or `<https://arxiv.org/abs/1806.09870>`_) we use:
::
......@@ -233,7 +235,7 @@ If you use the stochastic dynamics, we add the following entries to make sure we
To switch the simulation to AdResS this is the key part. This starts the AdResS runs.
::
; AdResS parameters
adress = yes ;no
......@@ -275,14 +277,11 @@ ___________
.. Notice the syntax of a URL reference below `Text <URL>`_
.. .. literalinclude:: ./abrupt_adress.patch
:language: c
To apply the patch: (:ref:`abrupt_adress_patch`)
To apply the patch:
1) copy into the main directory (gromacs/)
2) patch < abrupt_adress.patch
The patch for Abrupt_AdResS can be found below, see reference :ref:`abrupt_adress`
2) patch < abrupt_adress.patch
.. Remember to change the reference "patch" for something unique in your patch file subpage or you will have
cross-referencing problems
......@@ -310,14 +309,7 @@ When *gmx mdrun* finished normally (with the above mentioned setup), we have sev
5) If we only thermalize the transition region, the AT region is NVE-like, which means it is even possible to determine the dynamics of the system.
The files for the water example can be found here:
:download:`spc-example.tar.gz <spc-example.tar.gz>`
:download:`<./spc-example.tar.gz>`_
The patch for the abrupt AdResS code is:
.. literalinclude:: ./abrupt_adress.patch
:linenos:
:download:`abrupt_adress <abrupt_adress.patch>`
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