maartensandbox

And with a PDB file, how can I make the atom names match exactly while also indicating that multiple hydrogen atoms are connected to the same molecule? For example, if...

I think I correctly implemented alanine for use with ff99 ``` ATOM 1 H1 ACE 1 2.000 1.000 -0.000 ATOM 2 CH3 ACE 1 2.000 2.090 0.000 ATOM 3 H2...

One more issue: ``` using Molly ff = MolecularForceField("ff14SB.xml"); sys = System("big_alanine.pdb",ff,boundary = CubicBoundary(1000.0u"nm"),rename_terminal_res = false) total_energy(sys,find_neighbors(sys)) ``` prints 1128.45113918646 kJ mol⁻¹ the python equivalent ``` import openmm from openmm...

that clarifies some stuff! I'm really struggling with basic things but from testing it looks like molly is at least a factor 10 faster than openmm (for my admittedly weird...

The plan is to wrap it up in a paper (though the draft is progressing slowly), so molly will definitely be cited! We really only need a way to evaluate...

> This sounds to me like there were issues when running inference. Then the results were not placed in “--out_dir results/user_predictions_small” Then they are not in the list when listdir...