simtk.org

Currently the only way I know how to simulate organic non-standard molecules is to use AMBER to make the inpcrd and prmtop with a box of explicit solvent.

Anyway to solvate them implicitly?

Thanks! -Jonathan

I'm not familiar with implicit models for any solvents other than water. That's not to say there aren't any, just that it's not a subject I'm familiar with. Perhaps someone else will know something.

Peter

Hi Peter, sorry for not being clear on this, i meant implicit water.

In amber you only can create a Born implicit water model with sander during the simulation process, which is not included in the free ambertools12.

What I need to do is load the inpcrd and prmtop files into OpenMM and have it run implicit water with a cutoff somehow.

Thanks, Jonathan

Just specify the implicit solvent model and cutoff when you call createSystem(). For example, prmtop.createSystem(implicitSolvent=OBC2, nonbondedCutoff=2*nanometers). See section 4.3.3 of the user guide.

Peter

Thank you for the reply, should have done more homework.

Made my simulations run 400x faster now and the results look good!!

Thank you so much!

We'll see if we can get it up to 401x in the next release.

Peter