Dear Hannes,
I am not really the right person to reply, as I've never used PUPIL, but it
has been around for a while and developed by one of the recognised 'expert'
groups in QM/MM application and development (Roitberg).
Google/pubmed/WoS will quickly bring up this publication, which has
further, relevant, information:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20915/abstract
A versatile AMBER-Gaussian QM/MM interface through PUPIL
Juan Torras1,*, Gustavo de M. Seabra2, Erik Deumens2, S. B. Trickey2
and Adrian E. Roitberg2,*
Abstract
The PUPIL package (Program for User Package Interfacing and Linking)
originally was developed to interface different programs for multiscale
calculations in materials sciences (Torras et al., J Comput Aided Mater Des
2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we
present an extension of PUPIL to computational chemistry by interfacing two
widely used computational chemistry programs: AMBER (molecular dynamics)
and Gaussian (quantum chemistry). The benefit is to allow the application
of the advanced MD techniques available in AMBER to a hybrid QM/MM system
in which the forces and energy on the QM part can be computed by any of the
methods available in Gaussian. To illustrate, we present two example
applications: A MD calculation of alanine dipeptide in explicit water, and
a use of the steered MD capabilities in AMBER to calculate the free energy
of reaction for the dissociation of Angeli's salt.
Juan Torras or Adrian Roitberg can probably point out more applications...
My question would be: is there a workflow/program included that does
macro-microiteration for QM/MM optimization? (i.e. energy minimization with
1 step QM, full MM convergence, 1 step QM, full MM convergence, etc.).
If it does, it would be a free (also outside the UK) alternative to
ChemShell (in addition to being able to use all the advanced simulation
methods in amber/sander).
--Marc
On 9 December 2014 at 07:42, <hannes.loeffler.stfc.ac.uk> wrote:
> Hi,
>
> this looks certainly interesting but from this email and the front page at
> sourceforge it is a bit unclear what exactly this code does. You say it is
> multi-scaling. In what sense? I spot there two MD codes and a few
> semiempirical/QM/etc codes. So I suspect you can do QM/MM type of
> calculations. What would be the advantage of your solution over existing
> ones? Are you primarily addressing developers?
>
> Many thanks,
> Hannes.
>
> ________________________________________
> From: Joan Torras [joan.torras.upc.edu]
> Sent: 08 December 2014 23:36
> To: amber.ambermd.org
> Subject: [AMBER] Software announcement: Release of PUPIL 3.0
>
> We are pleased to announce the release of PUPIL 3.0.
>
> PUPIL (Program for User Package Interface and Linking), is a software
> environment that allows users and developers to link quickly and
> efficiently together multiple pieces of software in a fully automated
> multi-scale simulation.
>
> * Graphic User Interface to build the main simulation input file.
> * Simulation Manager to lead the multi-scale simulation between
> different external programs.
> * Interface with Amber v10, 11, 12, and 14
> * Interface with DeMon2k 4.2.4
> * Interface with DL_CLASS_1.9 (DLPOLY)
> * Interface with NWChem v6.1.1 and v6.5
> * Interface with Gaussian 03 and 09
> * Interface with Siesta v3.2 (Start/Stop and CycleQM behaviors)
> * Interface with MNDO97 (Start/Stop QM role behaviors)
> * stubMD. Stub program for interface sample and testing playing a
> Molecular Dynamics Calculation Unit role.
> * stubQM. Stub program for interface sample and testing, playing a
> Cycle Quantum Mechanics Calculation Unit role.
> * stubDI. Stub program for interface sample and testing,playing an
> external Domain Identifier Calculation Unit role.
>
> New Features:
>
> * DL_CLASS program incorporates the electrostatic embedding scheme
> through the PUPIL interface.
> * PUPIL package has been updated to be compatible with Java 1.7 and 1.8.
> * A new interface with NWChem 6.3 and 6.5.
> * Some bottle-neck on the neighborhood rules has been fixed through the
> parallelization on the PUPIL core.
> * An initial alpha version using Long-range electrostatics on the QM
> region has been implemented
> * More accurate numerical checks are incorporated when the output files
> of tests cases are compared.
>
> For full details of PUPIL's features and capabilities, visit our web page:
>
> http://pupil.sourceforge.net/
>
>
> The PUPIL Team.
>
>
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> --
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Received on Tue Dec 09 2014 - 01:00:03 PST
