GitHub - scicrow/protocell-model: Pawsey internship with Ricardo Mancera for protocell membrane formation

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Pawsey internship with Ricardo Mancera for protocell membrane formation

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Name		Name	Last commit message	Last commit date
Latest commit History 54 Commits
0mm_myracid_charmm		0mm_myracid_charmm
DCA_CHARMM		DCA_CHARMM
amber-dopc		amber-dopc
analysis_scripts		analysis_scripts
archive		archive
build_scripts		build_scripts
ch_gui_core_files		ch_gui_core_files
ch_gui_dca_build		ch_gui_dca_build
ch_gui_lau_build		ch_gui_lau_build
ch_gui_myr_0mm		ch_gui_myr_0mm
charmm_bilayers		charmm_bilayers
charmm_builder		charmm_builder
charmm_memb		charmm_memb
dca_gromacs		dca_gromacs
gromacs_run		gromacs_run
job-submit-scripts		job-submit-scripts
job_checker		job_checker
keep_scripts		keep_scripts
lau_charmm		lau_charmm
lauric-0mM-charmm		lauric-0mM-charmm
mdp_scripts_231217		mdp_scripts_231217
my_gromacs_scripts		my_gromacs_scripts
packmol		packmol
r_drive_files		r_drive_files
run_core_files		run_core_files
run_library		run_library
testing_files		testing_files
topology_setup		topology_setup
DCA_CHARMM.7z		DCA_CHARMM.7z
README.txt		README.txt
map_R_drive_on_wsl.sh		map_R_drive_on_wsl.sh

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@Tom @Shani I have put the files for you projects on the R drive under R:\A-J\Biomolecular_Model-MANCER-HS00092\Origins_of_life\Lipid21-GAFF2_hybrid
We can start of reusing Jame's structure files for some of your systems (with a few tweaks), but you will need to eventually need to set up your own using Packmoi.
James' packmol files are under R:\A-J\Biomolecular_Model-MANCER-HS00092\Origins_of_life\JAMES_EXTRA\Documents\amber_systems\packmol_reorder\bilayer
December 12, 2023

Cara — 12/12/2023 5:18 PM
I've got a test system running on setonix in this folder: /scratch/pawsey0110/cara/origins_test/lipid21_hybrid/

bilayer directory is nucleotides and sugars for later simulation
LIPID21 directory is pulled from the R drive