Support for COM-pull, many-particle potential, checkpoint at regular intervals

[digvijaylp]

@smog-server I have incorporated few options to openSMOG. Details of the same are given below. There are basically two commits. In the first commit, COM-pull and custom many-particle potential were both included in contact section itself. In the second commit, I just moved those to a separate function with their separate x ml tags. Last two commits are just clean-up and some typo corrections in the comments.

The suggested update includes.

1. checkpoint reporter: which allows writing checkpoint at regular intervals.
2. function for defining COM restrain between group of atoms (like the pull-code option in GROMACS).
3. support for defining custom potential between >=2 particles. While this might not be useful in the context of output generated from the smog2, it will make the tool more accessible for people looking to try different potentials. say something in the format V = f(x_ij)*g(theta_ijk)

[digvijaylp]

@smog-server I am also including example input-files. this includes a harmonic COM-pull between 2 chains.
A custom torsion potential is defined in manyparticle section.
example.zip

[Whitford]

Thanks for the contribution. We will take a look at this and get back to you.

[digvijaylp]

update: PBC is not applied to bonded interactions in opeMM. the 10-12 contact pair potential in openSMOG is defined as CustomBondForce. Suggesting addition of setUsesPeriodicBoundaryConditions(True) to contacts forces.

[Whitford]

Digvijay,
Thank you for the excellent suggestion. In our testing, we were only considering cases where nonbonded terms need to be periodic. But, as you said, the bonded terms should be flagged as periodic, as well. We'll make the suggested improvement ASAP.

[Whitford]

Per your suggestion, we added PBC to custom contacts and torsions. See commit 7c5045
we are still working on appropriate tests to add to opensmogcheck, so it should still be considered experimental.

[Whitford]

FYI: we have added checks to opensmog-check, and the new PBC lines appear to be working as expected. Please let us know if you see anything unusual.

[Whitford]

thanks again for the suggestions. Based on your edits, I just introduced an option for using the checkpoint reporter routines. See commit 2d9b979