[WIP] Desmond System Test

Included in this PR are two system tests that compare OpenMM and Desmond in two ways. This isn't actually meant to be merged though.

**(1a)** Use desmond's tools to create a "desmond molecular system" (DMS) file that includes all of the parameters mapped onto all of the pairs, triplets, etc of atoms for ala2 in amber99sb-ildn in tip3p. Load this DMS file in OpenMM and  calculate the forces on every atom in the system.
**(1b)** Take the same geometry of ala2/tip3p, but setup the system in OpenMM from a pdb via OpenMM's `amber99sbildn.xml`

**These forces agree within 0.1 kcal/mol/nm**. I have done this test also on a larger system, and I know there are two sources of error. The first is that I think the templating of certain improper torsions that are declared in the amber forcefields with wildcards, like *, *, CT, NH is done slightly differently between OpenMM and `viparr`, which is desmond's system setup tool. The second source of error, I think, which is much smaller and the one that is active for this ala2 system, comes from some numerical issues with the nonbonded exceptions. This could be in 2 parts. One is that the setup of nonbonded exceptions requires converting coefficients for LJ forces specified with `a` and `b` as in `a/r^12 + b^6` to `sigma` and `epsilon` in the more "standard" way of writing the LJ force: this could introduce some small numerical issues. The second part of this error is that desmond lists the amber fudgeQQ parameter as 0.8333, whereas OpenMM uses two extras threes (0.833333). So there's some going to be some small difference there.

For the second test, I setup the system with desmond's templating engine (as in 1a), and then
**(2a)** Calculate the forces with desmond, by calling the desmond binary with the dms file.
**(2b)** Calculate the forces in OpenMM, from the dms file.

**Here, the forces do not agree**. But furthermore, the forces calculated *with desmond* using differtent PME cutoffs don't agree with one another. For example, here are the forces on the first three atoms in the system calculated with different PME cutoffs in OpenMM and Desmond. If you state at these numbers a little bit, you'll see that in the desmond numbers, there is a strong trend in which each of the forces move monotonically (by quite a bit) as you increase the cutoff. So clearly something is wrong with my desmond config file. If anyone has any ideas (cc: @leeping @kyleabeauchamp @jchodera) I'm all ears.

```
OpenMM nonbondedCutoff = 8 A
[[ 126.87218047  136.04450917   24.66186398]
 [  39.37468144  478.242654     68.87983042]
 [  32.79352221  -57.76740471  -53.52405496]]
OpenMM nonbondedCutoff = 9 A
[[ 127.02834782  136.24668641   24.6223779 ]
 [  38.54905691  478.211485     69.27124718]
 [  32.81578078  -57.57349163  -53.109029  ]]
OpenMM nonbondedCutoff = 10 A
[[ 126.9447592   136.19952351   24.71190588]
 [  38.64393074  478.064535     69.1117237 ]
 [  32.84153748  -57.85112691  -53.31015571]]
OpenMM nonbondedCutoff = 11 A
[[ 126.95114064  136.11638617   24.67819236]
 [  38.39931538  478.19056683   69.13630179]
 [  32.76650786  -57.72095102  -53.2609079 ]]
OpenMM nonbondedCutoff = 12 A
[[ 126.97312378  136.18475034   24.84544781]
 [  38.33276344  478.436878     68.93574197]
 [  32.82778515  -57.77204697  -53.30481262]]

Desmond nonbondedCutoff = 8 A
[[ 128.29093933  123.14955139   30.95908928]
 [ -13.34107208  504.97229004   38.50177002]
 [  41.41397095  -12.21356869  -48.0520668 ]]
Desmond nonbondedCutoff = 9 A
[[ 125.7900238   127.39439392   31.84701729]
 [  -7.42175341  501.32952881   36.75513458]
 [  45.25564957   -5.83741856  -47.85729599]]
Desmond nonbondedCutoff = 10 A
[[ 123.88157654  130.65797424   33.0093956 ]
 [  -3.13715291  498.11022949   34.66875458]
 [  48.03310013   -1.72448182  -48.11376953]]
Desmond nonbondedCutoff = 11 A
[[ 122.67459106  133.14651489   34.34104919]
 [  -0.69900793  495.22064209   32.1003685 ]
 [  50.16262054    1.20843768  -48.27210617]]
Desmond nonbondedCutoff = 12 A
[[ 121.91383362  135.07867432   35.75953674]
 [   0.50310475  492.65002441   29.18287659]
 [  51.81376266    3.28319073  -48.2746048 ]]
```