Bulk water example in the manual

[Mayank Vats]

Hello again Sean,

Could you share some sample indus.input files and plumed.dat files used to generate the example data in the indus manual?

I'm working with Gromacs 2019.4 and Plumed 2.5.3.

I've been trying to repeat that bulk-water calculation, for a 0.6nm radius cavity but at a Kappa of 0.98 kJ/mol with different values of x_star in the indus input file for even as low as -10; the output files still gives values of ~30 for N and N_tilde.

It would help to have a more step by step tutorial for the software in the manual or elsewhere.

[seanma...@gmail.com]

Hi, Mayank,

Sorry for the late response: the world got turned on its head no so long ago.

As mentioned in Sec. 7.1 of the manual, the input files used to generate the output you see can be found in the INDUS repo under indus/examples/bulk_water. I cannot speak to exactly why you see what you do, but it strikes me that your settings are not actually applying a bias on Ntilde-v, since its value is still roughly the same as at equilibrium in the unbiased ensemble.

What extra information would it be helpful to add to the manual/example? In the bulk water example, I believe I have added all of the information needed to reproduce the given results using any MD engine supported by PLUMED. While I do not provide my GROMACS input files, such information would be of little or no use to someone using e.g. LAMMPS or AMBER.

Sean

[seanma...@gmail.com]

I recall now that you posted this question at a time before I included the sample input files in the repo, which I did after discussions with you. Please let me know if you think of anything else that might be useful to add.