Published October 13, 2024
| Version v1
Model
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Molecular dynamics simulation files for PFAS-Polyamide membrane Potential of Mean Force
Description
Polyamide membrane is identical for all PFAS simulations: ~9 nm thick, charged. Compased of piperazine and trimesoyl chloride and 90% crosslinked.
PFAS explored are charged PFHxA, PFPeS, and GenX.
THe initial configurations of the PMF calculation: sys*.gro
Topology files: ligand.itp (PFAS), tip3p.itp (water,ion), swiss_mem2.top (membrane, system)
Simulation files: temper0.mpd (Step1: Tempering), npt_umb0.mdp (Step2: NPT relaxation at 300 K), and md_umb0.mdp (Step3: Umbrella sampling at 300K).
Scripts: run0.sh (simulation job script). convert.sh :converts *0.mdp to mpd files for each umbrella sampling window and run0.sh to job files for each window.
Files
Files
(676.9 MB)
| Name | Size | Download all |
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md5:bc42849e7e4aee4b4b41fcf98e22c9bc
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225.6 MB | Download |
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md5:d262bdb4f40fe0c49449d7022434ffec
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1.1 kB | Download |
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md5:42e954240a754124c2a8e6ff231c6b1a
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225.7 MB | Download |
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md5:bc6fc634876b6c14b342e2a1bd35227c
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225.6 MB | Download |