search

openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format
1 stars 3 forks source link

Validation efforts for force field conversion #5

Open dscerutti opened 4 years ago

dscerutti commented 4 years ago

In order to have assurance that Open Force Field represents Amber parameters in the correct manner, energy evaluations of Amber-minimized structures will be carried out in Amber and OpenMM simulation engines. A variety of tetrapeptides, larger than anything used in parameter conversion, will be constructed, taking every sequence permutation for consecutive residues, plus all types of capping groups. The energy minimizations in Amber will generate energy terms for non-bonded van-der Waal,s non-bonded electrostatic, and all types of valence terms for comparison to their equivalent outputs from OpenMM. As a second layer of testing, OpenMM engines can be applied to the energy-minimized conformations to verify that they cannot move the structures into significantly difference energy minima.

j-wags commented 4 years ago

Update: Current progress on this is in the top-level ConvertParameters.py and test_parameterize.py scripts. These are changing rapidly, so we're not committing static copies of the resulting OFFXML.

The data needed to run ConvertParameters.py can be generated by running one of the top-level GenerateX scripts. I'm not sure which of those is most current. If a script requires pmemd it can be replaced with sander. There was also a problem setting up ambpdb but I can't recall how we solved that.