Hello, I have a problem concerning a circa 600 atom simulation. When trying to apply a force field to correct the bond lengths, the programm slows down to a crawl and seems to be calculating. However, even after hours of letting it work, there is no progress. I tried running the same simulation wi…

It would help to know a bit more about what you’re trying to do. At the moment, Avogadro uses a single core for minimization and certainly it can be slow on larger molecules. On the other hand, I’ve definitely minimized large molecules (500-600 atoms) - it’s slow, but it happens. So I guess I’m n…

Sorry, I see that the Information I’ve given is a bit sparse. I’m trying to optimize the geometry using the ghemical fore field. I mostly just constrain the part of the molecule that is supposed to have fixed coordinates, using “fix selcted atoms”, then start the force field via the Auto Optimizati…

I wouldn’t recommend Ghemical. It’s an attempt to replicate the old Tripos 5.2 force field. We implemented it because there were no other open-source force fields at the time. IMHO, MMFF94 or UFF re much better choices. You’re not giving much detail on the molecule itself, but I’d guess that with …

Alright, turns out the issue had nothing to do with either the force field or the RAM. There was a mistake in the template I used, where two atoms were at the same spot. I have honestly no idea how to even achieve that, but apparently that breaks the simulation. I tried replicating the issue on a ne…

Glad to hear you figured it out. Yes, it would be helpful to have a command to show possible issues. My group has a grant that will be implementing some features like this, so I’ll add to the pile.

Home Install Guide

Avogadro Discussion

Molecule too big for force field calculation

General Discussion

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled

Hosting by DigitalOcean and Powered by Discourse Follow us on Bluesky or Mastodon