Support for implicit water for organic molecules?

[Jonathan Saboury]

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

[Peter Eastman]

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

[Jonathan Saboury]

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

[Peter Eastman]

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

[Jonathan Saboury]

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!

[Peter Eastman]

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

Peter