Commit 6996acb8 authored by Donal MacKernan's avatar Donal MacKernan

corrected yet again the links in readme.rst

parent 3bf1e2b3
......@@ -128,14 +128,14 @@ The source codes comprise the following 5 files
::
(1) A python code `chebychev-lambda-input.py <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/chebychev-lambda-input.py>`_ that generates the lambda values to be input into LAMMPS according to the users' choices of number of interpolation points and the
(1) A python code `chebychev-lambda-input.py <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/chebychev-lambda-input.py>`_ that generates the lambda values to be input into LAMMPS according to the users' choices of number of interpolation points and the
minimum value of lambda to be used as the domain of integration
(2) A LAMMPS script codes `noinsert_trimer_elec6.in <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/harmonic/templatev5_nokspace-noinsert_trimer_elec6.in>`_ that generates the data required for estimating the changes in free energy due to the insertion TIP3P water molecules using a standard cut-off respectively.
(3) One example of coordinate input files for LAMMPS: `example_lj403v2.lammps <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/harmonic/example_lj403v2.lammps>`_
(2) A LAMMPS script codes `noinsert_trimer_elec6.in <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/harmonic/templatev5_nokspace-noinsert_trimer_elec6.in>`_ that generates the data required for estimating the changes in free energy due to the insertion TIP3P water molecules using a standard cut-off respectively.
(3) One example of coordinate input files for LAMMPS: `example_lj403v2.lammps <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/harmonic/example_lj403v2.lammps>`_
and `example_lj3200b.lammps <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/bf6d646de33532e331407c89e1d78b1064e154f6/modules/PI/CORE/LJ/CLEAN-CODE/example_lj3200b.lammps>`_
(4) A python script `data-new8-thdy.py <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/data-new8-thdy.py>`_ that takes as input the thermodynamic integration output data from LAMMPS and uses it to compute the corresponding free energy change using thermodynamic integration.
(5) A python script `data-new8-mbar.py <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/data-new8-mbar.py>`_ that takes as input the MBAR output data from LAMMPS and uses it to compute the corresponding free energy change using MBAR
and `example_lj3200b.lammps <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/example_lj3200b.lammps>`_
(4) A python script `data-new8-thdy.py <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/data-new8-thdy.py>`_ that takes as input the thermodynamic integration output data from LAMMPS and uses it to compute the corresponding free energy change using thermodynamic integration.
(5) A python script `data-new8-mbar.py <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/data-new8-mbar.py>`_ that takes as input the MBAR output data from LAMMPS and uses it to compute the corresponding free energy change using MBAR
Compilation and Linking
_______________________
......@@ -213,14 +213,14 @@ Running the lammps scripts
The examples 1. and 2. use the initial coordinates consisting of 3200 atoms defined by the -var input_COORDINATES_file example_3200b.lammps option, whereas the examples 3. and 4. use the default coordinates of 400 atoms. The RUNTIME and RELAXATION_time are very short for testing purposes. For production runs, they should be at least ten times longer.
`data-new8-thdy.py <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/data-new8-thdy.py>`_
`data-new8-thdy.py <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/data-new8-thdy.py>`_
~~~~~~~~~~~~~~~~~~~~~~~~~
This python code takes as input the thermodynamic integration output data from LAMMPS and uses it to compute the corresponding free energy change using thermodynamic integration. The user should call it from the directory where the output data from LAMMPS is held. It expects output data fo have the format header-name.tdy.number.dat where number equals the number of lambda values excluding zero. Here it is assumed that one particle is inserted. It will print the estimates of the free energy of insertion or deletion and also creates a director called TDY
and subdirectories where the results of the analysis are stored.
`data-new8-mbar.py <https://gitlab.e-cam2020.eu/mackernan/Classical-MD-Modules/blob/PIhydration/modules/PI/HYDRATION/CORE/data-new8-mbar.py>`_
`data-new8-mbar.py <https://gitlab.e-cam2020.eu/mackernan/particle_insertion/blob/master/PIhydration/data-new8-mbar.py>`_
~~~~~~~~~~~~~~~~~~~~~~~~
This python code takes as input the multiple Bennet Acceptance Ratio (MBAR) output data from LAMMPS and uses it to compute the corresponding free energy change using the pymbar code from the Chodera lab. The user should call it from the directory where the output data is held. It expects output data fo have the format header-name.mbar.number.dat where number equals the number of lambda values including zero. Here it is assumed that one particle is inserted. It will print the estimates of the free energy of insertion or deletion and also creates a director called MBAR and subdirectories where the results of the analysis are stored.
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