Commit 70b8aec9 authored by Alan O'Cais's avatar Alan O'Cais

Make spell check pass

parent 4f13fddb
......@@ -3,7 +3,7 @@ image: umbrellium/sphinx-doc
spelling:
script:
- pip install codespell
- codespell --skip=".git,_static,_build,Diff*" --quiet-level=2
- codespell --skip=".git,_static,_build,Diff*,*.patch" --quiet-level=2 --ignore-words-list="adress"
only:
- master
- merge_requests
......
......@@ -142,7 +142,7 @@ Here is a short manual on how to run the test and set up AdResS simulations in G
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>`_).
4) The next step is to create a double resolution configuration and adjust the dependencies (force field, topology, index file, GROMACS input file). Creating the configuration is straight forward (we use `<http://www.votca.org/home>`_).
::
......@@ -155,7 +155,7 @@ Of course, if you want to use this configuration in a MD simulation you have to
[ virtual_sites3 ]
; Site from funct a d
; atom depedencies func a b
; atom dependencies func a b
4 1 2 3 1 0.05595E+00 0.05595E+00
The next step is to adjust the status of the CG particle in the topology file (in our example: *topol.top*) from *A* for *atom* to *V* as *virtual particle*. And of course insert the new force field.
......@@ -246,7 +246,7 @@ Here you define the geometry of the atomistic region, either *sphere* (a spheric
adress_type = sphere ;xsplit sphere or constant
This defines the width of the atomistic region, starting from the given reference coordinate (keyword *adress_reference_coords*, by simpy using: *tail conf_hybrid.gro | awk '(NF==3){print $1/2., $2/2., $3/2.}'*). In the older versions of AdResS, with a smooth coupling between AT and CG the width of the hybrid region width (*adress_hy_width*) was also defined. In the Abrupt_AdResS setup it is not necessary any more, even if you put a number that region is counted (in the code) as AT.
This defines the width of the atomistic region, starting from the given reference coordinate (keyword *adress_reference_coords*, by simply using: *tail conf_hybrid.gro | awk '(NF==3){print $1/2., $2/2., $3/2.}'*). In the older versions of AdResS, with a smooth coupling between AT and CG the width of the hybrid region width (*adress_hy_width*) was also defined. In the Abrupt_AdResS setup it is not necessary any more, even if you put a number that region is counted (in the code) as AT.
::
......@@ -287,7 +287,7 @@ To apply the patch: (:ref:`abrupt_adress_patch`)
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 nessecary 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).
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.
......
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