choderalab / saltswap-results

Repository for the results of saltswap that are necessary for a first publication

saltswap-results

This repository contains the analysis and simulation scripts used for the manuscript

@article{saltswap,
    author = {Gregory A. Ross, Ari\"{e}n S. Rustenburg, Patrick B. Grinaway, Josh Fass, and John D. Chodera.},
    title = {Biomolecular simulations under realistic macroscopic salt conditions},
    journal = {bioRxiv},
    doi = {10.1101/226001}
    year = {2017},
}

Current and historical versions of the simulation code used to produce this data can be found at https://github.com/choderalab/saltswap/

saltswap-results's Issues

Draft and iterate outline

Alchemical free energy calculation for adding a single salt pair to a box of water.

This is to validate the SAMS calibration free energy for the first ion pair.

DCD files don't save box vectors

We should move away from storing output as DCD files, since these don't store box vectors (causing major issues with trying to visualize counterion distributions around the biomolecule).

Run a number of equilibrium simulations at different chemical potentials

This can be used to calibrate the chemical potential.

Use SAMS to calculate the free energy to add many salt molecules to a box of water.

This can be used to calibrate the chemical potential. Also perform simulations with different water box sizes to test box size dependence.

Update saltswap-analysis_environment.yml

@gregoryross : Can you update the recommended analysis environment to contain the version of saltswap you used for the calculations? It currently says:

  - saltswap==0.1.dev0

Figure 7 is missing x-axis labels

@gregoryross : Figure 7 is missing x-axis labels

Decide on a stable storage system for saltswap simulation data

This repo should provide a stable way to read/write the saltswap simulation data such that results produced are fully reproducible and as self contained as possible.

For every nth iteration, I need to (at least) store:

• Total energy
• Volume
• System configurations (PDB files would be fine)
• Acceptance rates for insertion/deletion
• Work to insert/delete salt, along with the corresponding initial number of salt molecules and proposed final number
• The identities of each molecule (i.e. either water, Na+ or Cl-)

Calculate the sampling efficiency of ion concentration for a range of NCMC switching times.

Simulations to be performed at a fixed chemical potential. The most efficient switching time to be used in all subsequent simulations.

Regenerate figures from new DCD trajectories that contain box vectors

This is just a reminder to regenerate figures following #16 being fixed.