Work plan

[ramess101]

This is a list of the simulations we need to run

Put a * next to high priority tasks Put your initials next to a task that you are currently working on

Saturation viscosity

New list of compounds

C12H26

• [x] Potoff (SMR: done)

• [x] TraPPE

• [x] TAMie

C16H34 (not working)

• [ ] Potoff

• [ ] TraPPE

• [ ] TAMie

C22H46

• [ ] Potoff

• [ ] TraPPE (SMR: running)

• [ ] TAMie

22DM-butane (probably won't run this)

• [ ] Potoff

• [ ] TraPPE

23DM-butane

• [x] Potoff

• [x] TraPPE

• [x] TAMie

3-methylpentane

• [x] Potoff

• [x] TraPPE

• [x] TAMie

Old list of compounds

C2H6

• [ ] Potoff

• [ ] TraPPE

• [x] TAMie

• [ ] Exp-6

• [x] TraPPE-2

• [ ] MCMC 12-6

• [x] MCMC 13-6

• [x] MCMC 14-6

• [x] MCMC 15-6

• [x] MCMC 16-6

C3H8

• [x] Potoff

• [x] TraPPE

• [x] TAMie

• [ ] Exp-6

• [x] MCMC 14-6 (low priority)

• [x] MCMC 16-6

C4H10

• [x] Potoff

• [x] TraPPE

• [x] TAMie

• [ ] Exp-6

• [ ] MCMC 14-6 (low priority)

• [x] MCMC 16-6

C8H18

• [x] Potoff

• [x] TraPPE

• [x] TAMie

• [ ] Exp-6

• [ ] MCMC 14-6 (low priority)

• [ ] MCMC 16-6

IC4H10

• [x] Potoff

• [x] TraPPE

• [x] TAMie (SMR: Results are very similar to TraPPE)

• [x] AUA4

IC5H12

• [x] Potoff

• [x] TraPPE

• [x] TAMie

IC6H14

• [x] Potoff (SMR: Done. Ran again due to wrong previous Potoff parameters for IC6)

• [x] TraPPE

• [x] TAMie

IC8H18

• [x] Potoff

• [x] TraPPE

NEOC5H12

• [x] Potoff

• [x] TraPPE

• [x] AUA4

Finite size effects

C3H8, Potoff:

• [x] N100
• [x] N200
• [x] N400
• [x] N800

C4H10, Potoff:

• [x] N100
• [x] N200
• [x] N400
• [x] N800

C4H10, TraPPE:

• [x] N200
• [x] N400
• [x] N800

C8H18, TraPPE:

• [x] N200
• [x] N400
• [x] N800

IC8H18, TraPPE:

• [x] N200
• [x] N400
• [x] N800

Simulation length

C8H18, TraPPE, N400

Saturation

• [x] 0.5 ns
• [x] 1 ns
• [x] 2 ns
• [x] 4 ns

High pressure

• [x] 1 ns
• [x] 2 ns
• [x] 4 ns

Harmonic bonds

TraPPE, N400

• [x] C3H8

• [x] C4H10

• [x] C8H18

High pressure

293 K

TraPPE, N400

• [x] C3H8

• [x] C4H10

• [x] C8H18

• [x] IC5H12

• [ ] 3MPentane (SMR: Running)

Potoff, N400

• [x] C3H8

• [x] C4H10

• [x] C8H18

TAMie, N400 (high priority)

• [x] C3H8

• [x] C4H10

• [x] C8H18

MCMC Mie 16-6, N400

• [x] C3H8

• [ ] C4H10

• [ ] C8H18

MCMC Mie 14-6, N400

• [ ] C3H8

• [ ] C4H10

• [ ] C8H18

347 K

TraPPE, N400, C8H18 (Validation)

• [x] Harmonic

• [x] LINCS

[ramess101]

@mostafa-razavi

The previous comment was for simulations. This list is for scripts that need to be written or modified.

Shell scripts

• [x] Harmonic bonds

• [ ] Variable simulation length

• [ ] Include exponential-6

• [ ] Use different directory hierarchy when not using MCMC

• [ ] General branched alkanes script with harmonic bonds and/or finite size effects

• [ ] Separate force field script to improve readability

Python scripts

GreenKubo_analyze

• [x] Improve fit for high viscosity

• [x] More robust uncertainty quantification

• [x] Fit standard deviation to model

• [x] Speed-up uncertainty analysis

• [x] Compare multiple force fields on same plot

• [x] Use Maginn's heuristic for determining tcut

Pre-simulation files

• [x] Creates initial simulation conditions from REFPROP

[ramess101]

SURF Student (Michelle Anderson, @Kaiveria ) Tasks

Short-term:

1. Walk through code with me:

   • [x] Saturated viscosity scripts
   • [x] Gromacs input files
   • [x] Pre-simulation python
   • [x] Post-simulation python

2. Walk through work plan

   • [x] Recap what has already been done
   • [x] Talk about what needs to still be done

3. Get set up to run jobs:

   • [x] Get access to calc1, md1
   • [x] Clone GitHub repository

4. Figure out dihedrals:

   • [x] Validate that we are implementing alkane dihedrals correctly

   • [ ] Determine how to implement the AUA4m dihedral model (very low priority now)

5. Validate n-octane TraPPE results from literature

   • [x] NVT ensemble only

     • [x] Simulate fixed bonds

     • [x] Simulate harmonic bonds

   • [x] NPT followed by NVT

     • [x] Simulate fixed bonds

     • [x] Simulate harmonic bonds

6. NPT ensemble

   • [x] Include NPT equilibration and production steps

   • [x] Determine which barostat to use and other parameters

   • [x] From average density, create new box for NVT ensemble

• [x] 7. Make branchedAlkane simulations more robust

• [x] 8. Pull REFPROP values for higher pressures (T293highP)

• [x] 9. Create T293highP conditions files for each molecule

• [x] 10. Reanalyze (GreenKubo_analyze.py) the state points where the uncertainties are inordinately large

• [x] 11. Modify T293highP script so that it includes NPT first

• [x] 12. Include RDF computation for high pressure runs

• [x] 13. Simulate isooctane at high pressures at 293 K (check that script works on md1)

• [x] 14. Move beyond Berendsen barostat

• [x] 15. Modify branchedAlkanes_SaturatedViscosity so that restarts whenever gromacs returns error

• [x] 16. Create .top and .gro files for challenge compound

• [x] 17. Create .top and .gro files for additional branched alkanes similar to challenge compound, i.e. 2,2,5-trimethylhexane, 2,4,4-trimethylhexane

• [x] 18. Extract TDE data and correlations for 2,2,4-trimethylhexane, 2,2,5-trimethylhexane, 2,4,4-trimethylhexane

• [x] 19. Create exponential-6 directory and files

• [x] 20. Allow for variable simulation time lengths, or at least longer simulations at higher pressures

• [ ] 21. Create generalized script

• [ ] 22. Saturation conditions at lower temperatures (i.e. near triple point), see propane for example

• [ ] 23. Run nOctane, T347highP, TraPPE, harmonic, with NPT first on calc1 (make sure NPT production uses correct thermostat, barostat and taup)

• [x] 24. Run IC4H10, T293highP, TraPPE, LINCS, NPT first on md1 (make sure NPT production uses correct thermostat, barostat and taup)

• [x] 25. Run IC8H18, T293highP, Potoff, LINCS, NPT first, 4 ns on md1 (make sure NPT production uses correct thermostat, barostat and taup) we need be able to set the nsteps in NVT_vis. I would use 1 ns for the lowest pressure, 2 ns for the next two pressures, and 4 ns for the top two pressures.

• [x] 26. Repeat 24. and 25. but with the different force fields. IC4H10 can do TraPPE, Potoff, TAMie, and AUA4. IC8H18 will just have TraPPE and Potoff.

Long-term:

• [ ] Finish running saturation jobs

• [ ] Start running high pressure simulations

• [ ] Nonequilibrium molecular dynamics (NEMD)

• [x] Test simulation length