Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 15 Dec 2014 17:42:06 -0500

Hi Morgan,

On Mon, Dec 15, 2014 at 3:17 PM, Lawrenz, Morgan <mlawrenz.amgen.com> wrote:
>
> Hi all,
> I want to perform a gas-phase protein simulation (to compare with gas
> phase structural biology experiments) using the AMOEBA ff.
>

​Then​

​I'm afraid you'll have to use another software. The alternative is to
introduce a large periodic box​ with no solvent, but then you will still
have the periodic images of the solute interacting with each other.

​But I only think PME is supported for the multipole force in the Amoeba
force field (someone will hopefully correct me if I'm wrong).​ Alternative
softwares capable of this calculation include Tinker and OpenMM, if I'm not
mistaken (the latter of which you've probably had perhaps a passing
acquaintance with ;).

Good luck, and I hope all is going well,
Jason​

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 15 2014 - 15:00:02 PST
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