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Iermi peg paper - #1698
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iermi wants to merge 19 commits into
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Iermi peg paper#1698iermi wants to merge 19 commits into
iermi wants to merge 19 commits into
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125 PGME molecules and 441 water molecules
125 PGME molecules and 686 water molecules
125 PGME and 1028 water molecules
These are pdb-files which can be used later with openmm for simulating systems from the paper.
Added a README file explaining the PEG paper files and their parameters.
Corrected a typographical error in the README.
This script converts GROMACS topology and coordinates into OpenMM format, checking for missing coordinates and periodic box information.
Added forcefield.itp file for OPLS-AA force field with references and defaults.
Here are files which are listed in OPLS AA force field folder of Gromacs software
run_open_mm.py is the file for running the simulation similar to the one used in Gromacs. The set up can be later incorporated in MDMC to derived the force field parameters
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Description of work
Added a new molecule and non-equilibrated boxes with di-propylene glycol methylene ether
Fixes
Not a fix
To test
One can try to see if these boxes are ok to be run on the laptop. I will also provide bigger and smaller booxes