Yes, this should be possible. ForceBalance works by passing force field files to other MD codes (e.g. OpenMM or Gromacs) and reading their outputs, so as long as you can create a force field file to give pair interactions, you should be in business.ponadto wrote:OK, ForceBalance works like a charm, but at the moment I only had time to check the 001_water_tutorial.
I have a different project and I was wondering if I could ForceBalance for a quite different purpose than the one we were discussing so far.
I'll ask a few questions without thoroughly reading the doc:
1. Can I use ForceBalance to parameterize pair interactions between (any) two groups of atoms?
Your system is indeed larger than the ones I've tackled. I don't think it's outside the scope of ForceBalance though I haven't done a calculation of this size before. I think the main limitations will come from array size, as ForceBalance stores a number of large arrays in memory. Some arrays are size (3*N_atoms*N_parameters*N_snapshots), others are (9*N_atoms^2), and others are (3*N_atoms*N*parameters*N_parameters). Some of these large arrays are allocated in order to speed up the calculation in other ways, but they aren't 100% necessary. Thus, I would suggest first trying with a small number of snapshots and then increasing it.ponadto wrote:2. My system is quite large (~1000 atoms), and the two groups of atoms I'm considering both consist of 5 amino-acid residues. Also, my full atom trajectory is long (say, 10^6 snapshots). Would that be palpable for ForceBalance?
Have I overinterpreted the features of ForceBalance, or am I still in the scope of potential usage?
Also, ForceBalance is intended to be usable for large systems, so if you do run into problems with system size I would be happy to improve the code to address these issues.
Let me know if this is something you're interested in, I think it would be a medium-sized project in itself.