Project ID: plumID:19.021
Name: Coarse-Grained Directed Simulation
Archive: https://github.com/hockyg/CGDS-Paper/raw/master/CGDS_JCTC_2017_HockyEtAl.zip
Category: methods
Keywords: experiment directed simulation, coarse-grain, bias
PLUMED version: 2.5b
Contributor: Glen Hocky
Submitted on: 29 Apr 2019
Last revised: 01 May 2019
Publication: G. M. Hocky, T. Dannenhoffer-Lafage, G. A. Voth, Coarse-Grained Directed Simulation, Journal of Chemical Theory and Computation 13, 4593–4603 (2017)

PLUMED input files

File Compatible with
…5ns.flatten_us_k10000.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…75ns.flatten_us_k1000.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…75ns.flatten_us_k5000.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…75ns.flatten_us_k5000.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…175ns.flatten_us_k500.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…175ns.flatten_us_k500.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.15ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…q175ns.range10_init0.100ps.run.20000000.plumed.dat tested on v2.5 tested on master
…_eq175ns.range10_init0.5ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.25ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…_eq175ns.range10_init0.5ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.50ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.15ps.run.20000000.plumed.dat tested on v2.5 tested on master
…_eq175ns.range10_init0.1ps.run.20000000.plumed.dat tested on v2.5 tested on master
…q175ns.range10_init0.100ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.30000000.plumed.dat tested on v2.5 tested on master
…_eq175ns.range1_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.40000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…_eq175ns.range1_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range1_init0.100ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range1_init0.100ps.run.20000000.plumed.dat tested on v2.5 tested on master
…_eq175ns.range1_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.20ps.run.20000000.plumed.dat tested on v2.5 tested on master
…q175ns.range10_init0.100ps.run.40000000.plumed.dat tested on v2.5 tested on master
…eq175ns.range10_init0.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…s.range1_init0_lm001.100ps.run.20000000.plumed.dat tested on v2.5 tested on master
…ns.range1_init0_lm001.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…5ns.range1_init0_lm01.10ps.run.20000000.plumed.dat tested on v2.5 tested on master
…ns.range1_init0_lm01.100ps.run.20000000.plumed.dat tested on v2.5 tested on master
…5ns.range1_init0_lm0.100ps.run.10000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.80000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.90000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.70000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.20000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.60000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.30000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.50000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.40000000.plumed.dat tested on v2.5 tested on master
…k5000/actin-gatpu_ionized.run.100000000.plumed.dat tested on v2.5 tested on master
…_k5000/actin-gatpu_ionized.run.10000000.plumed.dat tested on v2.5 tested on master
…b_k500/actin-gatpu_ionized.run.20000000.plumed.dat tested on v2.5 tested on master
…b_k500/actin-gatpu_ionized.run.30000000.plumed.dat tested on v2.5 tested on master
…b_k500/actin-gatpu_ionized.run.10000000.plumed.dat tested on v2.5 tested on master
…traflat_i100ps_lm0.01_p100.run.10000000.plumed.dat tested on v2.5 tested on master
…traflat_i100ps_lm0.01_p100.run.60000000.plumed.dat tested on v2.5 tested on master
…traflat_i100ps_lm0.01_p100.run.10000000.plumed.dat tested on v2.5 tested on master

Last tested: 18 Aug 2019, 14:17:26

Project description and instructions
Everything should be self-explanatory with run scripts in tar file. Used GROMACS 5.1.X. This tar contains all inputs and analysis scripts for the paper. Figures can be generated with included Python2 Jupyter notebooks after producing data.

Submission history
[v1] 29 Apr 2019: original submission
[v2] 01 May 2019: fix path files

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