Add 12-6-4 support for the Energy/Emin/Ene_Decomp commands in cpptraj

[pengfeili1]

Hi Dan,

Finally I found a time to add the 12-6-4 support to the Energy/Emin/Ene_Decomp commands in cpptraj on GitHub. Can you approve this pull request? Thanks!

Best,
Pengfei

[drroe]

This looks great Pengfei!

If it's not too much trouble, can you please add a test case that calculates 12-6-4 energies? I went a slightly different route in my new branch for adding LJ C parameters, and when I'm merging your code in I want to make sure I don't break anything.

If you'd rather I just merge this in I can do that and we can add the test cases after.

[drroe]

I'll just go ahead and merge this for now and work on adding some tests. I also need to increment the version number.

Thanks again!

[drroe]

@pengfeili1 I wasn't able to reproduce the VDW energies I get in sander with the VDW energies that CPPTRAJ produces when LJ C coefficients are present (although the 1-4 terms look OK). Can you please take a look? I'm attaching a tarball that contains the topology and restart I am testing with, along with a script to run everything. Let me know if you need anything else.
CannotReproduceLj1264.tar.gz

[drroe]

One note - to better reproduce the total electrostatic energy between sander/cpptraj decrease the direct sum tolerance in both to 0.00001

[drroe]

FYI I started adding LJ 12-6-4 to my version 7 branch (https://github.com/drroe/cpptraj/tree/prepareforleap.remote.buildatom) using your previous commit #1159 as notes and I'm testing against sander as I go. I will hopefully have it done tomorrow.