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

From: Lawrenz, Morgan <mlawrenz.amgen.com>
Date: Mon, 15 Dec 2014 22:52:13 +0000

Thanks for the help Jason! I will check out OpenMM for this!
Best!
Morgan


-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, December 15, 2014 2:42 PM
To: AMBER Mailing List
Subject: Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER

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 - 15:00:03 PST
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