Implement of soft bond potential

[kexul]

Dear Sire Developers: This is an implementation of soft bond potential , including the following changes:

1. Added a new perturbation type called ScalePerturbation to take care of the exclusion list changes during ring open/close. The exclusion list changes are found by biosimspace, I'll create a PR later.
2. Decoupled the LJ and coulomb scale parameters from the 14 interactions, so they could be interpolated by lambda.
3. Implemented the soft bond potential function for bond perturbation.

I've tested the Fxa series in the paper mentioned above, here is the result:	pair	soft-bond run1	soft-bond run2	soft-bond run3	current	exp	schrodinger
4c->edo	-1.36515025	-1.579566	-1.599211	-4.11	-0.8	-1.48
4d->edo	-1.1339635	-0.99799	-1.238629167	-3.29	-0.87	-1.69
edo->4c	2.0459925	2.1593732	1.834021	5.8	0.8	1.48
edo->4d	2.04595	1.2482862	0.824815167	1.18	0.87	1.69

From the overlap matrix and pmf plot, we could see that the ring open/close is well treated:

Overlap matrix of current implementation:

PMF of current implementation:

Overlap matrix of soft-bond potential:

PMF of soft-bond potential:

Looking forward to your comments!

[jmichel80]

Hi @kexul many thanks for undertaking this significant piece of work. I will need some time to review carefully the implementation before I comment on the technical approach

[kexul]

It's my pleasure to contribute to this great open source project. 😄 More tests are underway, I'll post updates here.

[kexul]

TPSB2 series (mean and std obtained by three runs) :

pair	soft-bond	current imp	exp	schrodinger
mol1->mol2	0.74±0.03	1.15±0.10	0.62	0.16
mol2->mol1	-0.81±0.07	-1.29±0.17	-0.62	-0.16