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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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Address issues raised by Xubo lin with incorrect conversion to desmond #320

Closed mrshirts closed 7 years ago

mrshirts commented 7 years ago

Add more documentation of problem.

mrshirts commented 7 years ago

Looks like one of the issues is that UB energies are being classified as angle in GROMAS and bond in desmond. 

            type     input(gromacs)  output (desmond)    diff (desmond)
           angle     31631.03693255    22880.93486112    -8750.10207143
            bond      6172.06789834    14922.14114872     8750.07325038
    urey_bradley         0.00000000        0.00000000        0.00000000

There also appears to be an issue with the dihedrals, which appears to be in the impropers conversion to dihedrals. I need to take a look at those more closely. 

        improper       374.97923319        0.00000000     -374.97923319
        dihedral     22328.89078369    21953.90589696     -374.98488673

And the charges and van der Waals values appear fine.

      coulomb-14    110056.19801743   110056.20293920        0.00492177
          vdw-14      4515.57521096     4515.57626792        0.00105696
mrshirts commented 7 years ago

These were both reporting issues, addressed by a PR to https://github.com/ctk3b/InterMol/pull/1