[AMBER] Box with a “separator”

From: Alessandro Mariani <alessandro.mariani.uniroma1.it>
Date: Tue, 2 Apr 2019 11:59:01 +0200

Hello Amber users and developers.
I’d like to simulate a system physically divided in two (or more) compartments. In the first compartment there is a “Solution A”, made of water and some other larger molecules, in all the other sectors, only water is there. Now, the box should be physically separated by a “wall” with some nano-pores, to allow possible diffusion from Solution A to the rest of the box. My first idea was to use a grraphene sheet including some restraints to avoid undesired rotations (floating). The problem is that I am not able to create a prep file for such a large sheet (50x50 Å^2). Do you have any advise for:

1) obtain a suitable prep file for the graphene sheet
2) a different “separator” that I can use?

Best regards


Alessandro Mariani, PhD
HIU - Helmholtz-Institut Ulm für elektrochemische Energiespeicherung
KIT - Karlsruhe Institute of Technology

Office 311
Helmholtzstraße 11, 89081 Ulm - GERMANY
Phone: +49 (0) 731 50 34109

EMAIL: alessandro DOT mariani AT kit DOT edu
RESEARCHGATE: Alessandro Mariani
ORCID: 0000-0002-3686-2169
SCOPUS AUTHOR ID: 56346581000

www DOT hiu-batteries DOT com

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Received on Tue Apr 02 2019 - 03:00:02 PDT
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