Commit 3bec9533 authored by Christian Krekeler's avatar Christian Krekeler

adjusted dependencies

parent b92767ae
......@@ -19,13 +19,38 @@
Licence
Opensource
MD Simulation:
See GROMACS web page: `<http://www.gromacs.org>`_
Analysis tools and thermodynamic force calculation:
see VOTCA web page: `<http://www.votca.org/home>`_
Visualize Molecular Dynamics: `<http://www.ks.uiuc.edu/Research/vmd/>`_
Documentation Tool
none
Application Documentation
none
See GROMACS web page: `<http://www.gromacs.org>`_
See VOCTA web page: `<http://www.votca.org/Documentation>`_
Visualize Molecular Dynamics: `<http://www.ks.uiuc.edu/Research/vmd/>`_
Relevant Training Material
See GROMACS web page: `<http://www.gromacs.org>`_
See VOCTA web page: `<http://www.votca.org/tutorials>`_
Visualize Molecular Dynamics: `<http://www.ks.uiuc.edu/Research/vmd/>`_
Relevant Training Material
none
......@@ -87,7 +112,7 @@ Quick and fast data grab from the configuration file:
tail conf.gro | awk '(NF==3){print $1/2.0,$2/2.0,$3/2.0}'
How to mask the configuration for setting it up for the AdResS simulation:
How to mask the configuration for setting it up for the AdResS simulation. A straigh forward way is using `VOTCA <http://www.votca.org/tutorials>`_ :
::
......@@ -105,21 +130,21 @@ Check temperature on the fly from the output md.log:
paste mdlogging1 mdlogging2 >temperature
rm mdlogging1 mdlogging2
Quick grab of the density in the xsplit (slab like) configuration:
Quick grab of the density in the xsplit (slab like) configuration. One way is using the tool from `GROMACS <http://www.gromacs.org>`_:
::
gmx density -d X -f trajectory_file.xtc -sl 50
Quick grab of the density in the sphere configuration:
Quick grab of the density in the sphere configuration. We use `VOTCA <http://www.votca.org/tutorials>`_ for it:
::
csg_density -- axis r -- rmax 10. --ref [x_ref,y_ref,z_ref] --trj trajectory_input.xtc --top topol.tpr --out SOL.dens.out
Collect the p(N) data and combine them in one file:
Collect the p(N) data and combine them in one file. For that we use `VMD <http://www.ks.uiuc.edu/Research/vmd/>`_, it includes a script called topotools, which is used to handle the trajectory. This script can be run from the command line directly:
::
......@@ -142,7 +167,7 @@ And the corresponding extract_coord.tcl:
mol new conf.gro
mol addfile traj_comp.xtc type xtc waitfor all first 0 last -1 step 1
topo writevarxyz WCG.xyz selmod "name WCG and (x>285 and x<315)"
exit
All the small scripts are available as files:
......
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