GitHub - clauswilke/MACV_SMD: Code and data for Meyer et al, Analyzing Machupo virus-receptor binding by molecular dynamics simulations, PeerJ 2:e266 (2014).

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Code and data for Meyer et al, Analyzing Machupo virus-receptor binding by molecular dynamics simulations, PeerJ 2:e266 (2014).

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Name		Name	Last commit message	Last commit date
Latest commit History 68 Commits
eq_analysis		eq_analysis
fep_config		fep_config
fep_data		fep_data
figures		figures
smd_config		smd_config
smd_data		smd_data
smd_rmsf_data		smd_rmsf_data
README.txt		README.txt
Response_to_reviewers.odt		Response_to_reviewers.odt
Response_to_reviewers.pdf		Response_to_reviewers.pdf
abstract.txt		abstract.txt
diff.pdf		diff.pdf
diff.tex		diff.tex
full_paper.bib		full_paper.bib
full_paper.pdf		full_paper.pdf
full_paper.tex		full_paper.tex
paper.bib		paper.bib
paper.pdf		paper.pdf
paper.tex		paper.tex
peerj.bst		peerj.bst

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This file is meant to explain each of the top level directories.  There should be a similar readme in the relevant folders.

eq_analysis   - contains the scripts used to generate the equilibration rmsf plots as well as the plot themselves.
fep_config    - contains everything necessary to run the dual topology fep
fep_data      - contains the final data and analysis script for the fep simulations
figures       - contains all plots used in the manuscript along with pymol structures that were used at various points in development, the force curves, and the movies
smd_config    - contains everything necessary to run our smd pipeline
smd_data      - contains all data and scripts that we ever used in the preparation of this manuscript
smd_rmsf_data - contains all data and scripts used to generate the rmsf comparison plot