yes, I think so. Thank you!

Hi Peter, In response to my question last week you wrote: It depends on exactly what you want to do. - Which energy terms do you want to compute? - What do you want to do with energy terms that involve more than two atoms, such as angles and dihedrals? (If you use implicit solvent or a polarizable f...

I want to compute the potential energy due to a subset of water molecules in the system, maybe a couple hundred of them. I wouldn't need to do it at every MD step, just occasionally (this is to calculate thermo quantities so I just need good enough sampling). For one of the things I want to do I can...

Hi OpenMM, I want to analyze the potential energies due to some atoms in the system but not the rest. As in, if atom A is in the included group, all its interactions are counted toward the energy, including those with atoms B which may not be in the included group. Is there a way to do this without ...

Hi OpenMM, I am trying to use a gromacs-made topology to run simulations in openmm to take advantage of the faster CUDA code. My system consists of a protein, water/ions, urea, and TMAO. I need the TMAO and urea to be completely constrained bond-wise, the protein to be constrained only in the h-cont...

Got it, thank you Peter!

So the E in the numerator and denominator is the same (it's the current total energy at whatever temperature?), just the temperatures are different?

Hi OpenMM!

I am wondering what is the right way to reweight observables calculated from simulated tempering trajectories with the default weighting algorithm? Is reweighting even necessary? I am new to this technique so I apologize if the question is naive.

Thank you!
Dan

Hi OpenMM,

I want to do a simulation of a D-amino acid protein with the Amber force field in OpenMM. I realized that to do it completely correctly, I might need to flip some dihedral parameters in the protein.ff14SB.xml file. Is this true and if so what do I need to change and how?

Thank you!
Dan

Oh ok, thank you, I will use a bond force.