Results for Tyrosine-choline, Phenylalanine-choline and Tryptophan-choline force field improvements. For ease of processing, results from both works are kept together. Results are divided in QM calculations+force field comparison and improvements, and force field parameter validations.
If you have trouble navigating, please send email to reza.611@gmail.com.
Please see the file "file_organisations" for the directories and subdirectories.
Results files are organised based on QM calculations and force field comparisons (also improvements), and Parameters validations where you have the test cases. For the QM calculations, they are based on the softwares and methods used. PSI4 directories for energy decompositions and SAPT methods, further divided in subdiectories. NWCHEM is for all other QM methods, and those can be differentiated by the dircetoty names which contains the method (DFT, MP2, CCSD(T)) and basis sets. CHARMM* directories contains the force field comparison vs the improvements test.
The Khan_etal_JCTC_2016 paper contains phenol-TMA and benzene-TMA cases. The Khan_etal_JCTC_2019 contains the indole-TMA case.
For the QM part, benzene-tma and indole-tma directories have naming explicitly (i.e. NWCHEM_cat_pi_benzene_tma/, PSI4_calc_benzene_tma/, CHARMM_pes_cat_pi_benzene_tma/). For phenol-TMA, look at the *_RESTART directories; these are the production ones for CHARMM and NWCHEM cases. For PSI4, it is PSI4_calc/). Other directories are old tests with different PES conditions (relaxation etc.). I did not remove them for my personal reference.
For the Parameters validations, reboot_piplc-dmpc/ is the test case for Khan_etal_JCTC_2016; all others are for Khan_etal_JCTC_2019.
Manuscripts files are seperated for both these works in the main directories with submission files and figures. The raw data are also there. You will also find the raw data in the different results subdirectories.
*** I am writing this very quickly, so some explanations might not be obvious. If you have doubt, please send email to reza.611@gmail.com.
